Masp-2 inhibitors and methods of use

ABSTRACT

The present disclosure provides, inter alia, compounds with MASP-2 inhibitory activity, compositions of such compounds and methods of making and using such compounds.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of pending U.S. application Ser. No.16/425,791, filed May 29, 2019, which is a continuation of InternationalPatent Application No. PCT/US19/34220 filed May 28, 2019, which claimsthe benefit of U.S. Provisional Application Ser. No. 62/677,472, filedMay 29, 2018, U.S. Provisional Application Ser. No. 62/677,538, filedMay 29, 2018, U.S. Provisional Application Ser. No. 62/677,495, filedMay 29, 2018, and U.S. Provisional Application Ser. No. 62/677,514,filed May 29, 2018. Each of the foregoing related applications isincorporated herein by reference in its entirety.

STATEMENT REGARDING SEQUENCE LISTING

The sequence listing associated with this application is provided in.xml format in lieu of a paper copy and is hereby incorporated byreference into the specification. The name of the .xml file containingthe sequence listing is MP_1_0281_US2_SequenceListing_20221122_ST26. The.xml file is 2,641 bytes, was created on Nov. 22, 2022, and is beingsubmitted via the Patent Center with the filing of the specification.

FIELD

The present disclosure is directed generally to compositions and methodsthat are useful in the field of medicine. More specifically, thedisclosure provides small molecule synthetic inhibitors ofmannan-binding lectin-associated serine protease-2 (MASP-2), includingsmall molecule inhibitors that are selective for MASP-2 over thrombin,compositions thereof, and methods for the manufacture and use thereof.

BACKGROUND

The complement system plays a role in the inflammatory response andbecomes activated because of tissue damage or microbial infection.Complement activation must be tightly regulated to ensure selectivetargeting of invading microorganisms and avoid self-inflicted damage(Ricklin et al., Nat. Immunol. 11:785-797, 2010). Currently, it iswidely accepted that the complement system can be activated throughthree distinct pathways: the classical pathway, the lectin pathway, andthe alternative pathway. The classical pathway is usually triggered by acomplex composed of host antibodies bound to a foreign particle (i.e.,an antigen) and generally requires prior exposure to an antigen for thegeneration of a specific antibody response. Since activation of theclassical pathway depends on a prior adaptive immune response by thehost, the classical pathway is part of the acquired immune system. Incontrast, both the lectin and alternative pathways are independent ofadaptive immunity and are part of the innate immune system.

Mannan-binding lectin-associated serine protease-2 (MASP-2) has beenshown to be required for the function of the lectin pathway, one of theprincipal complement activation pathways (Vorup-Jensen et al., J.Immunol 165:2093-2100, 2000; Ambrus et al., J Immunol. 170: 1374-1382,2003; Schwaeble et al., PNAS 108:7523-7528, 2011). Importantly,inhibition of MASP-2 does not appear to interfere with theantibody-dependent classical complement activation pathway, which is acritical component of the acquired immune response to infection. Asdescribed in U.S. Pat. No. 9,011,860 (assigned to Omeros corporation),which is hereby incorporated by reference, discloses a fully humanmonoclonal antibody targeting human MASP-2 has been generated whichbinds to human MASP-2 with high affinity and blocks the lectin pathwaycomplement activity and is therefore useful to treat various lectincomplement pathway-associated diseases and disorders.

MASP-2-dependent complement activation has been implicated ascontributing to the pathogenesis of numerous acute and chronic diseasestates. Therefore, a need exists for small molecule compounds which aresuitable for administration for treatment of subject suffering fromMASP-2 complement pathway-associated diseases and disorders.

An important protein for mammalian immunity is the mannan-bindinglectin-associated serine protease-2 (MASP-2), which has been shown to berequired for the function of the lectin pathway, one of the principalcomplement activation pathways (Vorup-Jensen et al., J. Immunol165:2093-2100, 2000; Ambrus et al., J Immunol. 170: 1374-1382, 2003;Schwaeble et al., PNAS 108:7523-7528, 2011). Inhibition of MASP-2 doesnot appear to interfere with the antibody-dependent classical complementactivation pathway, which is a critical component of the acquired immuneresponse to infection. Inhibiting human MASP-2 to block the lectinpathway complement activity is useful to treat various lectin complementpathway-associated diseases and disorders.

Therapeutic compounds and methods of identifying small moleculeinhibitors of MASP-2 are needed as they are important to treat variouslectin complement pathway-associated diseases and disorders, includingdiseases that are not suitably or efficiently treated with largemolecule biologic inhibitors.

SUMMARY

The present disclosure provides, inter alia, compounds of Formulae (I-1)and (I-2):

or a salt thereof; wherein the variables are as defined below.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (I-1) or (I-2), or a pharmaceuticallyacceptable salt thereof, and at least one pharmaceutically acceptablecarrier or excipient.

The compounds of Formula (I-1) or (I-2) are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (I-1) or(I-2), or a salt thereof.

The present disclosure provides, inter alia, compounds of Formulae (IIA)and (IIB):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (IIA) or (IIB), are alsodescribed.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (IIA) or (IIB), or a pharmaceuticallyacceptable salt thereof, and at least one pharmaceutically acceptablecarrier or excipient.

The compounds of Formula (IIA) or (IIB) are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (IIA) or(IIB), or a salt thereof.

The present disclosure provides, inter alia, compounds of Formula (III):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (III), are also described.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (III), or a pharmaceutically acceptablesalt thereof, and at least one pharmaceutically acceptable carrier orexcipient.

The compounds of Formula (III) are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (III), or asalt thereof.

The present disclosure provides, inter alia, compounds of Formulae (IV):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (IV), are also described.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (IV), or a pharmaceutically acceptablesalt thereof, and at least one pharmaceutically acceptable carrier orexcipient.

The compounds of Formula (IV) are useful as MASP-2 inhibitors. Thecompounds of Formula (IV) are useful in therapy. The compounds ofFormula (IV) are useful in the treatment of MASP-2-associated diseasesand disorders, and in the manufacture of medicaments for treatingMASP-2-associated diseases and disorders. The present disclosure alsoprovides methods of treating a MASP-2-associated disease and disordercomprising administering to a patient a therapeutically effective amountof a compound of Formula (IV), or a salt thereof.

The present disclosure provides, inter alia, compounds of Formulae (VA)or (VB):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (VA) or (VB) are also described.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (VA) or (VB), or a pharmaceuticallyacceptable salt thereof, and at least one pharmaceutically acceptablecarrier or excipient.

The compounds of Formula (VA) and (VB) are useful as MASP-2 inhibitors.The compounds of Formula (VA) and (VB) are useful in therapy. Thecompounds of Formula (VA) and (VB) are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (VA) or (VB),or a salt thereof.

The present disclosure provides, inter alia, compounds of Formulae (VIA)or (VIB):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (VIA) or (VIB) are alsodescribed.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (VIA) or (VIB), or a pharmaceuticallyacceptable salt thereof, and at least one pharmaceutically acceptablecarrier or excipient.

The compounds of Formula (VIA) and (VIB) are useful as MASP-2inhibitors. The compounds of Formula (VIA) and (VIB) are useful intherapy. The compounds of Formula (VIA) and (VIB) are useful in thetreatment of MASP-2-associated diseases and disorders, and in themanufacture of medicaments for treating MASP-2-associated diseases anddisorders. The present disclosure also provides methods of treating aMASP-2-associated disease and disorder comprising administering to apatient a therapeutically effective amount of a compound of Formula(VIA) or (VIB), or a salt thereof.

The present disclosure provides, inter alia, compounds of Formulae(VIIA) or (VIIB):

or a salt thereof; wherein the variables are as defined below. Variousembodiments of the compounds of Formula (VIIA) or (VIIB) are alsodescribed.

The present disclosure also provides a pharmaceutical compositioncomprising a compound of Formula (VIIA) or (VIIB), or a pharmaceuticallyacceptable salt thereof, and at least one pharmaceutically acceptablecarrier or excipient.

The compounds of Formula (VIIA) and (VIIB) are useful as MASP-2inhibitors. The compounds of Formula (VIIA) and (VIIB) are useful intherapy. The compounds of Formula (VIIA) and (VIIB) are useful in thetreatment of MASP-2-associated diseases and disorders, and in themanufacture of medicaments for treating MASP-2-associated diseases anddisorders. The present disclosure also provides methods of treating aMASP-2-associated disease and disorder comprising administering to apatient a therapeutically effective amount of a compound of Formula(VIIA) or (VIIB), or a salt thereof.

The present disclosure provides, inter alia, small molecule compoundshaving MASP-2 inhibitory activity, especially for therapeutic use. Thesmall molecule compound with MASP-2 inhibitory activity interacts withthe MASP-2 serine protease domain in an enzyme-inhibitor complex with aplurality of intermolecular interactions. In certain aspects, the smallmolecule is described with complete specificity and description by thenumber and type(s) of intermolecular interactions within a MASP-2binding site, using an empirically derived rule set. The inhibitorsfollow one or more of the interaction rules.

In certain aspects, the present disclosure provides a small moleculecompound with MASP-2 inhibitory activity, for therapeutic use, whereinthe compound has one or more such as 1, 2, 3, 4, or 5 of the followinginteractions (a) to (e):

a) the compound binds via H-bonds with one or more of PRO 606, ASP 627,SER 628, ARG 630, SER 633, SER 654, GLY 656, SER 657, CYS 660 and GLN665 in MASP-2;

b) the compound binds via ionic or electrostatic interactions orhydrogen bonding to one or more of ASP 627 and ARG 630 in MASP-2;

c) the compound interacts via a water molecule in MASP-2 to one or moreof TYR 602, TYR 607, ASP 627, SER 628, SER 657, ASN 659, GLU 662, TRP655, GLY656, CYS660, GLN 665, TYR 666, VAL 668, and ARG 630 in MASP-2;

d) the compound interacts via π-π interactions with one or more of PHE529, TYR 607, and TRP 655 in MASP-2; and

e) the compound interacts via van der Waals contacts to one or more ofALA 468, ALA 469, HIS 483, ASP 526, ALA 527, GLY 528, PHE 529, LEU 575,PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS 629, ARG 630,GLY 631, ASP 632, SER 633, GLY 634, GLY 635, VAL 653, SER 654, TRP 655,GLY656, SER 657, MET 658, ASN 659, CYS 660, GLN 665, GLY 667, and TYR669 in MASP-2,

In some embodiments, the compound is not an endogenous MASP-2 ligand.

In some embodiments, the compound is a synthetic small molecule MASP-2inhibitor.

In some embodiments, the compound selectively inhibits MASP-2 ascompared to thrombin.

Various embodiments of the compounds defined by interaction rules aredescribed. The disclosure provides a composition comprising such acompound, or a pharmaceutically acceptable salt thereof, and at leastone pharmaceutically acceptable carrier or excipient. The compounds areuseful as MASP-2 inhibitors. The compounds are useful in therapy. Thecompounds are useful in the treatment of MASP-2-associated diseases anddisorders, and in the manufacture of medicaments for treatingMASP-2-associated diseases and disorders. The present disclosure alsoprovides methods of treating a MASP-2-associated disease and disordercomprising administering to a patient a therapeutically effective amountof a compound of defined by interaction rules set forth herein.

The present disclosure provides, inter alia, compounds of Formula(VIII):

or a salt thereof; wherein the elements of the Formula may have valuesas described below. Various embodiments of the compounds of Formula(VIII) are also described. The present disclosure also provides apharmaceutical composition comprising a compound of Formula (VIII), or apharmaceutically acceptable salt thereof, and at least onepharmaceutically acceptable carrier or excipient. The compounds ofFormula (VIII) are useful as MASP-2 inhibitors. The compounds of Formula(VIII) are useful in therapy. The compounds of Formula (VIII) are usefulin the treatment of MASP-2-associated diseases and disorders, and in themanufacture of medicaments for treating MASP-2-associated diseases anddisorders. The present disclosure also provides methods of treating aMASP-2-associated disease and disorder comprising administering to apatient a therapeutically effective amount of a compound of Formula(VIII), or a salt thereof.

The present disclosure provides, inter alia, a pharmacophore model fordescribing small molecule compounds including synthetic compounds thatinhibit MASP-2 and compounds defined with specificity by reference tosuch a pharmacophore model.

In some embodiments, the compounds that are active as inhibitors ofMASP-2 may include one or combinations of 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 of the pharmacophoreelements, preferably combinations of 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13or 14 of the pharmacophore elements listed in Table 1. In someembodiments, the compounds may have pharmacophore elements correspondingto those listed in Table 1, wherein the (x, y, z) coordinates of thepharmacophore elements are within four standard deviations, preferablywithin three standard deviations, more preferably within two standarddeviations and most preferably within one standard deviation as listedin Table 1.

In some embodiments, a compound is provided that comprises a combinationof pharmacophore elements comprising:

(a) an S1 pharmacophore group comprising CA1 and N1 pharmacophoreelements or CA1 and C5 pharmacophore elements; and/or

(b) an S2 pharmacophore group comprising H4 and O2 pharmacophoreelements; and/or

(c) an S3 pharmacophore group comprising a C2 pharmacophore element andan N2 or H3 pharmacophore element;

wherein:

C2 and C5 are hydrophobic groups;

CA1 is an aromatic ring;

H3 and H4 are hydrogen bond donors;

N1 and N2 are positive ionizable groups; and

O2 is a hydrogen bond acceptor;

wherein C2, C5, CA1, H3, H4, N1, N2, and O2 have coordinates in theranges given in Table 3, 4 or 5 below.

In some embodiments, a compound is provided that comprises a combinationof pharmacophore elements comprising:

(a) an S1 pharmacophore group comprising CA1 and N1 pharmacophoreelements or CA1 and C5 pharmacophore elements;

(b) an S2 pharmacophore group comprising H4 and O2 pharmacophoreelements; and

(c) an S3 pharmacophore group comprising a C2 pharmacophore element andan N2 or H3 pharmacophore element.

Various embodiments of the small molecule compounds defined by thepharmacophore model are described. The disclosure provides a compositioncomprising such a compound, or a pharmaceutically acceptable saltthereof, and at least one pharmaceutically acceptable carrier orexcipient. The compounds are useful as MASP-2 inhibitors. The compoundsare useful in therapy. The compounds are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of defined by thepharmacophore model.

The present disclosure also provides small molecule compounds withMASP-2 inhibitory activity, wherein the compound interacts with abinding site of MASP-2, wherein the compounds are defined by referenceto “binding rules” or “rule sets” derived using virtual docking modelsof crystallographically-derived MASP-2 enzyme co-crystal structures andbinding sites within the MASP-2 enzyme. In certain aspects, the aminoacids and their respective atoms of the MASP-2 binding site that areaccessible to small molecule MASP-2 inhibitors are described. By using avariety of compounds and their intermolecular interactions, it ispossible to design a set of “binding rules” or “rule set” by whichMASP-2 inhibitors are specifically described.

In certain aspects, an small molecule MASP-2 inhibitor is described by arule set. The compound with MASP-2 inhibitory activity interacts with abinding site of MASP-2 such as an enzyme-inhibitor complex, with aplurality of intermolecular interactions. In certain aspects, themolecule is described with complete specificity and a completedescription by the number and type(s) of in silico intermolecularinteractions between atoms of the MASP-2 amino acid residues of thebinding site and atoms of the inhibitor molecule. These rules areempirically derived using virtual docking models ofcrystallographically-derived MASP-2 enzyme co-crystal structures andbinding sites within the MASP-2 enzyme. In certain instances, aplurality of MASP-2 enzyme-inhibitor models can be used such as 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, or 30 or even more protein models togenerate a set of rules.

In some embodiments, the present disclosure provides a compound withMASP-2 inhibitory activity, wherein the compound interacts with abinding site, the interactions being one or more of (a) to (e):

a) the compound interacts via H-bonds with one or more amino acidresidues in the binding site of MASP-2 (SEQ ID NO: 1);

b) the compound interacts via ionic or electrostatic interactions orhydrogen bonding in the binding site of SEQ ID NO: 1;

c) the compound interacts via a water molecule in a binding site of SEQID NO: 1;

d) the compound interacts via π-π interactions with one or more aminoacid residues in the binding site of SEQ ID NO: 1; and/or

e) the compound interacts via van der Waals contacts to one or moreamino acid residues in the binding site of SEQ ID NO: 1, wherein thecompound is not an endogenous ligand or substrate.

In certain aspects, the compound has 1, 2, 3, 4, or 5 of theinteractions (a)-(e).

In another embodiment, the present disclosure provides a method foridentifying a small molecule capable of inhibiting MASP-2, comprising:

a) screening small molecule libraries using in silico docking forcandidate small molecules that are selectively identified for theirability to target and bind to MASP-2 at a binding site of a MASP-2model; and

b) testing/evaluating the candidate agents identified in step (a)through one or more in vitro assays for their ability to target and bindto a MASP-2 binding site, to thereby identify the small molecule capableof inhibiting MASP-2.

In certain aspects, the candidate small molecules comprise uniquechemical scaffolds as identified in step (b) and are optimized for theirability to inhibit MASP-2.

These and other aspects, objects and embodiments will become moreapparent when read with the detailed description and figures whichfollow.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1129) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 2 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1034) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 3 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1024) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 4 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1059) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 5 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1088) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 6 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1036) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 7 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1081) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 8 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1063) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 9 is a plot illustrating a schematic of one embodiment of the atomsof an inhibitory compound (1065) with those of MASP-2 amino acids ascomputed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 10 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1030) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 11 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1037) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 12 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1118) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 13 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1090) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 14 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1007) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 15 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1021) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters(3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 16 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1097) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å)employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 17 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound (1089) with those of MASP-2 amino acidsas computed by LigPlot+ software settings for hydrogen-bond calculationparameters (3.35 Å for maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å) employing models derived from the correspondingcrystallographic MASP-2-compound co-structures.

FIG. 18 is a plot illustrating a schematic of one embodiment of theatoms of an inhibitory compound melagatran with those of MASP-2 aminoacids as computed by LigPlot+ software settings for hydrogen-bondcalculation parameters (3.35 Å for maximum distance between hydrogenbond donor and acceptor; and non-bonded contact parameters betweenhydrophobic to any contacts, such as van der Waals interactions withmaximum contact distance of 3.90 Å) employing models derived from thecorresponding crystallographic MASP-2-compound co-structures.

FIG. 19 is a plot showing the binding of compound (14) to MASP-2 showinghydrogen bonds as computed by LigPlot+ software.

FIG. 20 is a plot showing the binding of compound (54) to MASP-2 showinghydrogen bonds as computed by LigPlot+ software.

FIG. 21 is a plot showing the binding of compound (1042) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 22 is a plot showing the binding of compound (2018) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 23 is a plot showing the binding of compound (1149) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 24 is a plot showing the binding of compound (1031) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 25 is a plot showing the binding of compound (1153) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 26 is a plot showing the binding of compound (1025) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 27 is a plot showing the binding of compound (1012) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 28 is a plot showing the binding of compound (1078) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 29 is a plot showing the binding of compound (1145) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 30 is a plot showing the binding of compound (1050) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 31 is a plot showing the binding of compound (1253) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 32 is a plot showing the binding of compound (1257) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 33 is a plot showing the binding of compound (1297) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 34 is a plot showing the binding of compound (1304) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 35 is a plot showing the binding of compound (1306) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 36 is a plot showing the binding of compound (1307) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 37 is a plot showing the binding of compound (1328) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 38 is a plot showing the binding of compound (1334) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 39 is a plot showing the binding of compound (1335) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 40 is a plot showing the binding of compound (1338) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 41 is a plot showing the binding of compound (1345) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 42 is a plot showing the binding of compound (1351) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 43 is a plot showing the binding of compound (1353) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 44 is a plot showing the binding of compound (1360) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 45 is a plot showing the binding of compound (1367) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 46 is a plot showing the binding of compound (1368) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 47 is a plot showing the binding of compound (1371) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 48 is a plot showing the binding of compound (1372) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 49 is a plot showing the binding of compound (1373) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 50 is a plot showing the binding of compound (1492) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 51 is a plot showing the binding of compound (1399) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 52 is a plot showing the binding of compound (1406) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 53 is a plot showing the binding of compound (1411) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 54 is a plot showing the binding of compound (1433) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 55 is a plot showing the binding of compound (1435) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 56 is a plot showing the binding of compound (1441) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 57 is a plot showing the binding of compound (1450) to MASP-2showing hydrogen bonds as computed by LigPlot+ software.

FIG. 58 is a plot depicting melagatran bound to thrombin.

FIG. 59 is a plot showing melagatran bound to thrombin overlaid with aMASP-2 selective compound (1065) bound to MASP-2.

FIG. 60 is a plot showing compound (1065) bound to the SP domain ofMASP-2.

FIG. 61 is a plot showing compound (1334) bound to thrombin.

FIG. 62 is a plot showing compound (1334) bound to the SP domain ofMASP-2.

FIG. 63 is a plot showing compound (1334) bound to MASP-2 overlaid withcompound (1334) bound to thrombin.

FIG. 64 is a plot illustrating the S3-S4 binding pockets of MASP-2.

FIG. 65 is a plot illustrating the S3-S4 binding pockets of thrombin.

FIG. 66 is a plot showing a representation of the MASP-2 bindingsub-pockets.

FIG. 67 is a depiction of the distances between pharmacophore elementsdescribing the S1 and S2 regions. The S2 region comprises H4, O1, O2 andCA6. The S1 region area consists of H2, O4, CA1, C3, C5, C7, and N1.Distances mentioned in the text are shown.

FIG. 68 is a plot depicting the angles between pharmacophore elementsdescribing the S1 and S2 region.

FIG. 69 is a plot depicting the definitions of torsion angles used inthe text.

FIG. 70 is a plot depicting the definitions of torsion angles used inthe text.

FIG. 71 is a plot depicting the definitions of torsion angles used inthe text.

FIG. 72 is a plot depicting the distances between pharmacophore elementsdescribing the S2, S4 and RM region.

FIG. 73 is a plot depicting the definitions of angles used in the text.

FIG. 74 is a plot depicting the definitions of torsion angles used inthe text.

FIG. 75 is a plot depicting the definitions of torsion angles used inthe text.

FIG. 76 is a flow chart illustrating one embodiment of a process of thisdisclosure.

FIGS. 77A and 77B illustrate various interactions between a compound ofFormula VIIIA and the MASP-2 active site.

DESCRIPTION I. Definitions

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. In addition, the materials, methods, andexamples are illustrative only and not intended to be limiting.

In the Summary above, the present Description, and the claims below,reference is made to particular features and aspects of the invention,including method steps. The disclosure of the invention in thisspecification includes all possible combinations of such particularfeatures within the embodiments of the invention disclosed, at least tothe extent that such combinations are non-contradictory. For example, ifthe description presents aspects A, B, and C of an embodiment, it isunderstood that this also discloses particular embodiments includingboth aspects A and B, both aspects B and C, and both aspects A and C, aswell as an embodiment with aspects A, B, and C.

a. General Definitions

The terms “a,” “an,” or “the” not only include aspects with one member,but also include aspects with more than one member. For instance, thesingular forms “a,” “an,” and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “acell” includes a plurality of such cells and reference to “the agent”includes reference to one or more agents known to those skilled in theart.

The terms “about” and “approximately” refer to an acceptable degree oferror for the quantity measured given the nature or precision of themeasurements. Typical, exemplary degrees of error are within 20 percent(%); preferably, within 10%; and more preferably, within 5% of a givenvalue or range of values. Any reference to “about X” specificallyindicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X,1.01X, 1.02X, 1.03X, 1.04X, and 1.05X. Thus, “about X” is intended toteach and provide written support for a claim limitation of, e.g.,“0.98X.” Alternatively, in biological systems, the terms “about” and“approximately” may mean values that are within an order of magnitude,preferably within 5-fold, and more preferably within 2-fold of a givenvalue. Numerical quantities given herein are approximate unless statedotherwise, meaning that the term “about” or “approximately” can beinferred when not expressly stated. When “about” is applied to thebeginning of a numerical range, it applies to both ends of the range.Thus, “from about 5 to 20%” is equivalent to “from about 5% to about20%.” When “about” is applied to the first value of a set of values, itapplies to all values in that set. Thus, “about 7, 9, or 11 mg/kg” isequivalent to “about 7, about 9, or about 11 mg/kg.”

The term “MASP-2” refers to mannan-binding lectin-associated serineprotease-2. Human MASP-2 protein with UniProt accession code O00187 (SEQID NO:1). The Serine Protease Domain (‘B-chain’=Mannan-binding lectinserine protease 2 B chain, based on UniProtKB—O00187 (MASP-2_HUMAN))includes residues 445 to 686 (or consists of residues 445 to 686).

The term “MASP-2-dependent complement activation” refers toMASP-2-dependent activation of the lectin pathway, which occurs underphysiological conditions (i.e., in the presence of Ca⁺⁺) leading to theformation of the lectin pathway C3 convertase C4b2a and uponaccumulation of the C3 cleavage product C3b subsequently to the C5convertase C4b2a(C3b)n.

The term “MASP-2-dependent complement-associated disease or disorder”refers to a disease or disorder that is associated with MASP-2-dependentcomplement activation.

The term “MASP-2-associated disease or disorder” refers to a disease ordisorder that is associated with activation or activity of MASP-2,including MASP-2-dependent complement-associated disease or disorders,and wherein inhibition of MASP-2 is or is expected to be therapeuticallybeneficial.

The term “lectin pathway” refers to complement activation that occursvia the specific binding of serum and non-serum carbohydrate-bindingproteins including mannan-binding lectin (MBL), CL-11 and the ficolins(H-ficolin, M-ficolin, or L-ficolin).

The term “classical pathway” refers to complement activation that istriggered by an antibody bound to a foreign particle and requiresbinding of the recognition molecule Clq.

Amino acid residues are abbreviated as follows: alanine (Ala; A),asparagine (Asn; N), aspartic acid (Asp; D), arginine (Arg; R), cysteine(Cys; C), glutamic acid (Glu; E), glutamine (Gln; Q), glycine (Gly; G),histidine (His; H), isoleucine (Ile), leucine (Leu), lysine (Lys; K),methionine (Met; M), phenylalanine (Phe; F), proline (Pro; P), serine(Ser; S), threonine (Thr; T), tryptophan (Trp; W), tyrosine (Tyr; Y),and valine (Val; V).

In the broadest sense, the naturally occurring amino acids can bedivided into groups based upon the chemical characteristic of the sidechain of the respective amino acids. By “hydrophobic” amino acid ismeant either His, Leu, Met, Phe, Trp, Tyr, Val, Ala, Cys or Pro. By“hydrophilic” amino acid is meant either Gly, Asn, Gln, Ser, Thr, Asp,Glu, Lys, Arg or His. This grouping of amino acids can be furthersub-classed as follows: by “uncharged hydrophilic” amino acid is meanteither Ser, Thr, Asn or Gln. By “acidic” amino acid is meant either Gluor Asp. By “basic” amino acid is meant either Lys, Arg or His.

The term “conservative amino acid substitution” is illustrated by asubstitution among amino acids within each of the following groups: (1)glycine, alanine, valine, leucine, and isoleucine, (2) phenylalanine,tyrosine, and tryptophan, (3) serine and threonine, (4) aspartate andglutamate, (5) glutamine and asparagine, and (6) lysine, arginine andhistidine.

The term “a subject” includes all mammals, including without limitation,humans, non-human primates, dogs, cats, horses, sheep, goats, cows,rabbits, pigs and rodents.

The terms “small molecule” and “small organic molecule” refers to asmall carbon-containing molecule that has a molecular weight of about2500 daltons or lower. In some embodiments, a small molecule has amolecular weight of about 2000 daltons or lower. In some embodiments, asmall molecule has a molecular weight of about 1500 daltons or lower. Insome embodiments, a small molecule has a molecular weight of about 1000daltons or lower. In some embodiments, a small molecule has a molecularweight of about 750 daltons or lower. In some embodiments, a smallmolecule has a molecular weight of about 500 daltons or lower. In someembodiments, a small molecule has a molecular weight of about 50 daltonsor greater. In some embodiments, a small molecule has a molecular weightof about 75 daltons or greater. In some embodiments, a small moleculehas a molecular weight of about 100 daltons or greater. In someembodiments, a small molecule has a molecular weight of about 150daltons or greater. In some embodiments, a small molecule has amolecular weight of about 250 daltons or greater. In some embodiments,small molecules may have a molecular weight in the range from about 50daltons to about 500 daltons, from about 50 daltons to about 750daltons, from about 50 daltons to about 1000 daltons, from about 50daltons to about 1500 daltons, from about 50 daltons to about 2000daltons, or from about 50 daltons to about 2500 daltons. When the term“compound” is used herein, the term is explicitly intended to includesmall molecule compounds as defined herein (including any of theembodiments thereof).

The phrase “pharmaceutically acceptable” is employed herein to refer tothose compounds, materials, compositions and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

The terms “disorder,” “disease,” and “condition” are usedinterchangeably for a condition in a subject. A disorder is adisturbance or derangement that affects the normal function of the bodyof a subject. A disease is a pathological condition of an organ, a bodypart, or a system resulting from various causes, such as infection,genetic defect, or environmental stress that is characterized by anidentifiable group of symptoms.

The term “effective amount” or “effective dose” means an amountsufficient to achieve the desired result and accordingly will depend onthe ingredient and its desired result. Nonetheless, once the desiredeffect is identified, determining the effective amount is within theskill of a person skilled in the art.

The term “subcutaneous administration” refers to administration of aformulation under all layers of the skin of a subject.

The term “histidine” specifically includes L-histidine unless otherwisespecified.

The term “isotonic” refers to a formulation that has essentially thesame osmotic pressure as human blood. Isotonic formulations willgenerally have an osmotic pressure from about 250 to about 350 mOsmol/L.Isotonicity can be measured using a vapor pressure or freezing pointdepression osmometer, for example.

The term “hypertonic” refers to a formulation with an osmotic pressureabove that of human (i.e., greater than 350 mOsm/L).

The term “hydrogen-bonding” is a partially electrostatic attractionbetween a hydrogen (H) which is bound to a more electronegative atomsuch as nitrogen (N) or oxygen (O) and another adjacent atom bearing alone pair of electrons. For example, when it is stated that the nitrogenacts as a “hydrogen bond donor” it means that a hydrogen (H) bound to anitrogen (N) is donated by the nitrogen as it electrostaticallyattracted to or accepted by an adjacent atom bearing a lone pair ofelectrons such as an oxygen. Similarly, when it is stated that an oxygenacts as a “hydrogen bond acceptor,” it means that a hydrogen (H) boundto a more electronegative atom such as nitrogen (N) is electrostaticallyattracted to or “accepted by” an adjacent atom such as oxygen bearing alone pair of electrons. Sometimes the hydrogen bonded atoms are calledout without explicitly stating the origin and presence of anintermediate hydrogen atom. The term “hydrogen bonding” is used whereverLigPlot+ software predicts a hydrogen bonding interaction using itsalgorithm and applied parameters of 3.35 Å for maximum distance betweenhydrogen bond donor and acceptor. Not all hydrogen bonds may actually bein place simultaneously; this is evident for atoms that are shown toform 4 putative hydrogen bonds, where however, at any given time only 3hydrogen bonds are chemically possible. In general, although crystalstructures such as the co-crystal structural information herein does notdirectly show or detect hydrogen bonding, the software used to describethe co-crystal does predict such H-bonding exists. Therefore, throughoutthe disclosure when a H-bond is present and described, it may be said tobe “predicted” by software to be present.

The term ionic bonding includes a type of chemical bond that involvesthe electrostatic attraction between oppositely charged ions, and is theprimary interaction occurring in ionic compounds.

The term “van der Waals” interaction includes weak, short-rangeelectrostatic attractive forces between uncharged molecules, arisingfrom the interaction of permanent or transient electric dipole moments.As determined by LigPlot+ software employing models derived from thecorresponding crystallographic MASP-2 compound co-structures, suchinteractions include all contacts that are computed using non-bondedcontact parameters between hydrophobic to any contacts for interactionswith a maximum contact distance of 3.90 Å.

The term “π-π interaction or π-π stacking” interaction includesattractive, noncovalent interactions between aromatic rings that areoriented either roughly parallel or roughly perpendicular (such as in“edge-face” interactions) to each other, since they contain π bonds.

Typically, the active site of serine proteases such as MASP-2 is shapedas a cleft where the polypeptide substrate or inhibitor binds. Schechterand Berger labeled amino acid residues from the N to C terminus of thepolypeptide substrate as follows: Pi, . . . , P3, P2, P1, P1′, P2′, P3′,. . . , Pj) and their respective binding sub-sites Si, . . . , S3, S2,S1, S1′, S2′, S3′, . . . , Sj. The cleavage is catalyzed between P1 andP1′ (Schechter, I. & Berger, A. On the size of the active site inproteases. I. Papain. Biochem. Biophys. Res. Commun. 27 (1967)).

The term “binding site” is an area on the protein wherein a smallmolecule can interact with such as a region on the surface of MASP-2,which region does not or only partially overlaps with the active site,but nevertheless render the MASP-2 molecule less active or inactive.

The term “or” refers to an alternative and should in general beconstrued non-exclusively. For example, a claim to “a compositioncomprising A or B” would typically present an aspect with a compositioncomprising both A and B. “Or” should, however, be construed to excludethose aspects presented that cannot be combined without contradiction(e.g., a composition pH that is between 9 and 10 or between 7 and 8).

The group “A or B” is equivalent to the group “selected from the groupconsisting of A and B.”

The linking term “comprising” or “comprise” is not closed. For example,“a composition comprising A” must include at least the component A, butit may also include one or more other components (e.g., B; B and C; B,C, and D; and the like). The term “comprising” therefore should ingeneral be construed as not excluding additional ingredients. Forexample, a claim to “a composition comprising A” would covercompositions that include A and B; A, B, and C; A, B, C, and D; A, B, C,D, and E; and the like.

The term “hypertonic” refers to a formulation with an osmotic pressureabove that of human (i.e., greater than 350 mOsm/KglHhO).

The term “agent” refers to a compound or mixture of compounds that, whenadded to a composition, tend to produce a particular effect on thecomposition's properties. For example, a composition comprising athickening agent is likely to be more viscous than an otherwiseidentical comparative composition that lacks the thickening agent.

A “subject” includes all mammals, including without limitation, humans,non-human primates, dogs, cats, horses, sheep, goats, cows, rabbits,pigs and rodents.

A “synthetic” compound means a compound that is not naturally occurringand that has been synthesized by humans. Reference to a compound hereinmay be understood to include reference to synthetic compounds, unlessthe context indicates otherwise.

The terms “treat,” “treating,” or “treatment” includes administering orapplying a composition (e.g., a composition described herein) in anamount, manner (e.g., schedule of administration), and mode (e.g., routeof administration) that is effective to improve a disorder or a symptomthereof, or to prevent, to retard, or to slow the progression of adisorder or a symptom thereof. Such improvements can include, but arenot limited to, alleviation or amelioration of one or more symptoms orconditions, diminishment of the extent of a disease, stabilizing (i.e.,not worsening) the state of disease, prevention of a disease'stransmission or spread, delaying or slowing of disease progression,amelioration or palliation of the disease state, diminishment of thereoccurrence of disease, and remission, whether partial or total andwhether detectable or undetectable.

“Treating” and “treatment” also include prophylactic treatment. Incertain embodiments, treatment methods comprise administering to asubject a therapeutically effective amount of an active agent. Theadministering step may consist of a single administration or maycomprise a series of administrations. The length of the treatment perioddepends on a variety of factors, such as the severity of the condition,the age of the subject, the concentration of active agent, the activityof the compositions used in the treatment, or a combination thereof. Itwill also be appreciated that the effective dosage of an agent used forthe treatment or prophylaxis may increase or decrease over the course ofa particular treatment or prophylaxis regime. Changes in dosage mayresult and become apparent by standard diagnostic assays known in theart. In one aspect, chronic administration may be required. For example,the compositions are administered to the subject in an amount, and for aduration, sufficient to treat the subject.

The expressions, “ambient temperature” and “room temperature,” as usedherein, are understood in the art, and refer generally to a temperature,e.g., a reaction temperature, that is about the temperature of the roomin which the reaction is carried out, e.g., a temperature from about 20°C. to about 30° C.

b. Chemical Definitions

At various places in the present specification, certain features of thecompounds are disclosed in groups or in ranges. It is specificallyintended that such a disclosure include each and every individualsubcombination of the members of such groups and ranges. For example,the terms “C₁₋₆ alkyl” and “C₁-C₆ alkyl” are specifically intended toindividually disclose (without limitation) methyl, ethyl, C₃ alkyl, C₄alkyl, C₅ alkyl and C₆ alkyl.

At various places in the present specification, variables definingdivalent linking groups are described. It is specifically intended thateach linking substituent include both the forward and backward forms ofthe linking substituent. For example, —NR(CR′R″)_(n)— includes both—NR(CR′R″)_(n)— and —(CR′R″)_(n)NR— and is intended to disclose each ofthe forms individually. Where the structure requires a linking group,the Markush variables listed for that group are understood to be linkinggroups. For example, if the structure requires a linking group and theMarkush group definition for that variable lists “alkyl” or “aryl” thenit is understood that the “alkyl” or “aryl” represents a linkingalkylene group or arylene group, respectively.

The term “substituted” means that an atom or group of atoms formallyreplaces hydrogen as a “substituent” attached to another group. The term“substituted”, unless otherwise indicated, refers to any level ofsubstitution, e.g., mono-, di-, tri-, tetra- or penta-substitution,where such substitution is permitted. The substituents are independentlyselected, and substitution may be at any chemically accessible position.It is to be understood that substitution at a given atom is limited byvalency. The phrase “optionally substituted” means substituted orunsubstituted. The term “substituted” means that a hydrogen atom isformally removed and replaced by a substituent. A single divalentsubstituent, e.g., oxo, can replace two hydrogen atoms.

The terms “C_(n-m)” and “C_(n)-C_(m)” where n and m are integersindicates a group that contains from n to m carbon atoms. Examplesinclude C₁₋₄, C₁₋₆, and the like. The term is intended to expresslydisclose every member in the range, i.e., C_(n), C_(n+1), C_(n+2) . . .C_(m-2), C_(m-1), C_(m). For example, C₁₋₆ is intended to disclose C₁,C₂, C₃, C₄, C₅, and C₆. “C_(n-m)” means the same as “C_(n)-C_(m)”.

The term “alkyl” employed alone or in combination with other terms,refers to a saturated hydrocarbon group that may be straight-chain orbranched. The terms “C_(n-m) alkyl” and “C_(n)-C_(m) alkyl” refer to analkyl group having n to m carbon atoms. For example, C₁-C₁₂ indicatesthat the group may have from 1 to 12 (inclusive) carbon atoms in it. Ifnot otherwise indicated, an alkyl group about 1 to about 20 carbonatoms. An alkyl group formally corresponds to an alkane with one C—Hbond replaced by the point of attachment of the alkyl group to theremainder of the compound. In some embodiments, the alkyl group containsfrom 1 to 6 carbon atoms, from 1 to 4 carbon atoms, from 1 to 3 carbonatoms, or 1 to 2 carbon atoms. Examples of alkyl moieties include, butare not limited to, chemical groups such as methyl, ethyl, n-propyl,isopropyl, n-butyl, tert-butyl, isobutyl, sec-butyl; higher homologssuch as 2-methyl-1-butyl, 1,1-dimethylpropyl, n-pentyl, 3-pentyl,n-hexyl, 1,2,2-trimethylpropyl, hexyl, heptyl, octyl, nonyl, decyl,dodecyl, and the like. The term “lower alkyl” refers to alkyl groupshaving from 1 to 6 carbon atoms in the chain. A “substituted alkyl”group is an alkyl group that is substituted with one or moresubstituents.

The term “alkenyl” employed alone or in combination with other terms,refers to a straight-chain or branched hydrocarbon group correspondingto an alkyl group having one or more double carbon-carbon bonds. Analkenyl group formally corresponds to an alkene with one C—H bondreplaced by the point of attachment of the alkenyl group to theremainder of the compound. The terms “C_(n-m) alkenyl” and “C_(n)-C_(m)alkenyl” refer to an alkenyl group having n to m carbons. In someembodiments, the alkenyl moiety contains 2 to 6, 2 to 4, or 2 to 3carbon atoms. Example alkenyl groups include, but are not limited to,ethenyl, n-propenyl, isopropenyl, n-butenyl, sec-butenyl and the like.

The term “alkynyl” employed alone or in combination with other terms,refers to a straight-chain or branched hydrocarbon group correspondingto an alkyl group having one or more triple carbon-carbon bonds. Analkynyl group formally corresponds to an alkyne with one C—H bondreplaced by the point of attachment of the alkyl group to the remainderof the compound. The term “C_(n-m) alkynyl” and “C_(n)-C_(m) alkynyl”refer to an alkynyl group having n to m carbons. Example alkynyl groupsinclude, but are not limited to, ethynyl, propyn-1-yl, propyn-2-yl andthe like. In some embodiments, the alkynyl moiety contains 2 to 6, 2 to4, or 2 to 3 carbon atoms.

The term “alkylene”, employed alone or in combination with other terms,refers to a divalent alkyl linking group. An alkylene group formallycorresponds to an alkane with two C—H bonds replaced by points ofattachment of the alkylene group to the remainder of the compound. Theterm “C_(n-m) alkylene” refers to an alkylene group having n to m carbonatoms. Examples of alkylene groups include, but are not limited to,methylene, ethan-1,2-diyl, propan-1,3-diyl, propan-1,2-diyl,butan-1,4-diyl, butan-1,3-diyl, butan-1,2-diyl, 2-methyl-propan-1,3-diyland the like. In some embodiments, “C_(n-m) alkylene” can refer to chainof from n to m methylene (CH₂) groups, —(CH₂)n-m-, such as —CH₂—,—CH₂CH₂—, —CH₂CH₂CH₂—, etc.

The term “alkoxy”, employed alone or in combination with other terms,refers to a group of formula —O-alkyl, wherein the alkyl group is asdefined above. The term “C_(n-m) alkoxy” refers to an alkoxy group, thealkyl group of which has n to m carbons. Example alkoxy groups includemethoxy, ethoxy, propoxy (e.g., n-propoxy and isopropoxy), t-butoxy andthe like. In some embodiments, the alkyl group has 1 to 6, 1 to 4, or 1to 3 carbon atoms.

The term “alkoxyalkyl” refers to an alkyl group in which one or more ofthe hydrogen atoms has been replaced by an alkoxy group. The term“C_(n-m) alkoxy-C_(p)-q alkyl” refers to a C_(p-q) alkyl groupsubstituted by a C_(n-m) alkoxy group. In some embodiments, thehydroxyalkyl group has one alkoxy group. In some embodiments, thealkoxyalkyl group has one or two alkoxy groups, each on a differentcarbon atom. Examples may include, but are not limited to,methoxymethyl, ethoxymethyl, 3-ethoxyethyl, and 1-methoxyethyl.

The term “amino” refers to a group of formula —NH₂.

The term “carbamyl” refers to a group of formula —C(O)NH₂.

The term “carbonyl”, employed alone or in combination with other terms,refers to a —C(═O)— group, which also may be written as C(O).

The term “cyano” or “nitrile” refers to a group of formula —C—N, whichalso may be written as —CN.

The terms “halo” or “halogen”, used alone or in combination with otherterms, refers to fluoro, chloro, bromo and iodo. In some embodiments,“halo” refers to a halogen atom 10 selected from F, Cl, or Br. In someembodiments, halo is F.

The term “haloalkyl” refers to an alkyl group in which one or more ofthe hydrogen atoms has been replaced by a halogen atom. The term“C_(n-m) haloalkyl” refers to a C_(n-m) alkyl group having n to m carbonatoms and from at least one up to {2(n to m)+1} halogen atoms, which mayeither be the same or different. In some embodiments, the halogen atomsare fluoro atoms. In some embodiments, the haloalkyl group has 1 to 6 or1 to 4 carbon atoms. Example haloalkyl groups include CF₃, C₂F₅, CHF₂,CCl₃, CHCl₂, C₂Cl₅ and the like. In some embodiments, the haloalkylgroup is a fluoroalkyl group.

The term “haloalkoxy”, employed alone or in combination with otherterms, refers to a group of formula —O-haloalkyl, wherein the haloalkylgroup is as defined above. The term “C_(n-m) haloalkoxy” refers to ahaloalkoxy group, the haloalkyl group of which has n to m carbons.Example haloalkoxy groups include trifluoromethoxy and the like. In someembodiments, the haloalkoxy group has 1 to 6, 1 to 4, or 1 to 3 carbonatoms.

The term “hydroxyalkyl” refers to an alkyl group in which one or more ofthe hydrogen atoms has been replaced by a hydroxy. The term “C_(n-m)hydroxyalkyl” refers to a C_(n-m) alkyl group having n to m carbon atomsand from at least one hydroxy group. In some embodiments, thehydroxyalkyl group has one alcohol group. In certain aspects, thehydroxyalkyl group has one or two alcohol groups, each on a differentcarbon atom. In certain aspects, the hydroxyalkyl group has 1, 2, 3, 4,5, or 6 alcohol groups. Examples may include, but are not limited to,hydroxymethyl, 2-hydroxyethyl, and 1-hydroxyethyl.

The term “oxo” refers to an oxygen atom as a divalent substituent,forming a carbonyl group when attached to carbon, or attached to aheteroatom forming a sulfoxide or sulfone group, or an N-oxide group.

The term “sulfido” refers to a sulfur atom as a divalent substituent,forming a thiocarbonyl group (C═S) when attached to carbon.

The term “n-membered,” where n is an integer, typically describes thenumber of ring-forming atoms in a moiety where the number ofring-forming atoms is n. The term “n-m membered” wherein n and m areintegers describes a range where the number of ring forming atoms isfrom n to m. For example, piperidinyl is an example of a 6-memberedheterocycloalkyl ring, pyrazolyl is an example of a 5-memberedheteroaryl ring, pyridyl is an example of a 6-membered heteroaryl ringand 1,2,3,4-tetrahydro-naphthalene is an example of a 10-memberedcycloalkyl group.

The term “aromatic” refers to a carbocycle or heterocycle having one ormore polyunsaturated rings having aromatic character (i.e., having(4n+2) delocalized π (pi) electrons where n is an integer).

The term “aryl,” employed alone or in combination with other terms,refers to an aromatic hydrocarbon group, which may be monocyclic orpolycyclic (e.g., having 2, 3 or 4 fused rings). The term “C_(n)-m aryl”refers to an aryl group having from n to m ring carbon atoms. Arylgroups include, e.g., phenyl, naphthyl, anthracenyl, phenanthrenyl,indanyl, indenyl, tetracenyl, and the like. In some embodiments, arylgroups have from 6 to about 20 carbon atoms, from 6 to about 18 carbonatoms, from 6 to about 15 carbon atoms, or from 6 to about 10 carbonatoms. In some embodiments, the aryl group is phenyl.

The term “arylalkyl” or “aralkyl” or “alkylaryl” employed alone or incombination with other terms, refers to a group of formula-alkylene-aryl, and refers to an alkyl group as defined herein whereinat least one hydrogen has been replaced by an aryl group as definedherein. In some embodiments, arylalkyl is C₆₋₁₀ aryl-C₁₋₃ alkyl. In someembodiments, arylalkyl is C₆₋₁₀ aryl-C₁₋₄ alkyl. In some embodiments,arylalkyl is C₆₋₁₀ aryl-C₁₋₃ alkyl. In some embodiments, arylalkyl isphenyl-C₁₋₃ alkyl. Examples include, but are not limited to, benzyl,1-phenylethyl, 4-methylbenzyl, and 1,1,-dimethyl-1-phenylmethyl. In someembodiments, arylalkyl is benzyl.

The term “heteroaryl” or “heteroaromatic,” employed alone or incombination with other terms, refers to a monocyclic or polycyclicaromatic heterocycle having at least one heteroatom ring member selectedfrom sulfur, oxygen and nitrogen. An “n-membered heteroaryl” or“n-membered heteroaromatic”, wherein n is an integer, refers to aheteroaryl having n ring-forming atoms. An “n-m membered heteroaryl” or“n-m membered heteroaromatic”, wherein n and m are integers, refers to aheteroaryl having from n to m ring-forming atoms. The number of carbonatoms in the ring is fewer than the number of ring forming atoms by thenumber of heteroatoms. Thus, in some embodiments, an n-memberedheteroaryl may have n-1, n-2, n-3 or n-4 ring carbon atoms and an n-mmembered heteroaryl may have from n-1, n-2, n-3 or n-4 ring carbon atomsto m-1, m-2, m-3 or m-4 ring carbon atoms. In some embodiments, an n-mmembered heteroaryl may have from 1 to m-1 ring carbon atoms. In someembodiments, the heteroaryl ring has 1, 2, 3 or 4 heteroatom ringmembers independently selected from nitrogen, sulfur and oxygen. In someembodiments, any ring-forming N in a heteroaryl moiety can be anN-oxide. In some embodiments, the heteroaryl has 5-10 ring atomsincluding carbon atoms and 1, 2, 3 or 4 heteroatom ring membersindependently selected from nitrogen, sulfur and oxygen. In someembodiments, the heteroaryl has 5-6 ring atoms and 1 or 2 heteroatomring members independently selected from nitrogen, sulfur and oxygen. Insome embodiments, the heteroaryl is a five-membered or six-memberedheteroaryl ring. In other embodiments, the heteroaryl is aneight-membered, nine-membered or ten-membered fused bicyclic heteroarylring. Example heteroaryl groups include, but are not limited to,pyridine, pyrimidine, pyrazine, pyridazine, pyrrole, pyrazole, azolyl,oxazole, isoxazole, thiazole, isothiazole, imidazole, furan, thiophene,quinoline, isoquinoline, naphthyridine (including 1,2-, 1,3-, 1,4-,1,5-, 1,6-, 1,7-, 1,8-, 2,3- and 2,6-naphthyridine), indole, azaindole,benzothiophene, benzofuran, benzisoxazole, benzimidazole,imidazo[1,2-b]thiazole, purine, furazane, triazole, tetrazole,1,2,4-thiadiazole, quinazoline, phthalazine, imidazo[1,2-a]pyridine,imidazo[2,1-b]thiazolyl, or the like.

A five-membered heteroaryl ring is a heteroaryl group having five ringatoms wherein one or more (e.g., 1, 2 or 3) ring atoms are independentlyselected from N, O and S. Exemplary five-membered ring heteroarylsinclude thienyl, furyl, pyrrolyl, imidazolyl, thiazolyl, oxazolyl,pyrazolyl, isothiazolyl, isoxazolyl, 1,2,3-triazolyl, tetrazolyl,1,2,3-thiadiazolyl, 1,2,3-oxadiazolyl, 1,2,4-triazolyl,1,2,4-thiadiazolyl, 1,2,4-oxadiazolyl, 1,3,4-triazolyl,1,3,4-thiadiazolyl and 1,3,4-oxadiazolyl.

A six-membered heteroaryl ring is a heteroaryl group having six ringatoms wherein one or more (e.g., 1, 2 or 3) ring atoms are independentlyselected from N, O and S. Exemplary six-membered ring heteroaryls arepyridyl, pyrazinyl, pyrimidinyl, triazinyl and pyridazinyl.

The term “heteroarylalkyl,” employed alone or in combination with otherterms, refers to a group of formula -alkylene-heteroaryl. The term“n-membered heteroarylalkyl” wherein n is an integer refers to aheteroarylalkyl group in which the heteroaryl is n-membered. The term“n-m membered-C_(p-q)-alkyl” wherein n, m, p and q are integers refersto heteroarylalkyl group in which the heteroaryl is n to m membered andthe alkyl has from p to q carbon atoms. In some embodiments,heteroarylalkyl is 5-10 membered heteroaryl-C₁₋₃ alkyl or C₁₋₉heteroaryl-C₁₋₃ alkyl, wherein the heteroaryl portion is monocyclic orbicyclic and has 1, 2, 3, 4 or 5 heteroatom ring members independentlyselected from nitrogen, sulfur and oxygen. In some embodiments,heteroarylalkyl is C₁₋₉ heteroaryl-C₁₋₄ alkyl, wherein the heteroarylportion is monocyclic or bicyclic and has 1, 2, 3, or 4 heteroatom ringmembers independently selected from nitrogen, sulfur and oxygen.Examples include pyridylmethyl, such as 2-pyridylmethyl,3-pyridylmethyl, or 4-pyridylmethyl.

The term “cycloalkyl”, employed alone or in combination with otherterms, refers to a non-aromatic, saturated, monocyclic, bicyclic orpolycyclic hydrocarbon ring system. The term includes cyclized alkyl andalkenyl groups. The term “C_(n-m) cycloalkyl” refers to a cycloalkylthat has n to m ring member carbon atoms. Cycloalkyl groups can includemono- or polycyclic (e.g., having 2, 3 or 4 fused rings) groups andspirocycles. Cycloalkyl groups can have 3, 4, 5, 6 or 7 ring-formingcarbons (C₃₋₇). In some embodiments, the cycloalkyl group has 3 to 6ring members, 3 to 5 ring members, or 3 to 4 ring members. In someembodiments, the cycloalkyl group is monocyclic. In some embodiments,the cycloalkyl group is monocyclic or bicyclic. In some embodiments, thecycloalkyl group is a C₃₋₆ monocyclic cycloalkyl group. Ring-formingcarbon atoms of a cycloalkyl group can be optionally oxidized to form anoxo or sulfido group. Cycloalkyl groups also include cycloalkylidenes.In some embodiments, cycloalkyl is cyclopropyl, cyclobutyl, cyclopentylor cyclohexyl. Also included in the definition of cycloalkyl aremoieties that have one or more aromatic rings fused (i.e., having a bondin common with) to the cycloalkyl ring, e.g., benzo or thienylderivatives of cyclopentane, cyclohexane and the like. A cycloalkylgroup containing a fused aromatic ring can be attached through anyring-forming atom including a ring-forming atom of the fused aromaticring. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, 4,4-dimethylcyclohexyl, cycloheptyl,cyclopentenyl, cyclohexenyl, cyclohexadienyl, cycloheptatrienyl,norbornyl, norpinyl, norcarnyl, bicyclo[1.1.1]pentanyl,bicyclo[2.1.1]hexanyl, and the like. In some embodiments, the cycloalkylgroup is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl.

The term “cycloalkylalkyl,” employed alone or in combination with otherterms, refers to a group of formula -alkylene-cycloalkyl. The termC_(n-m) cycloalkyl-C_(p-q) alkyl wherein n, m, p and q are integers,refers to a cycloalkyl group having from n to m carbon atoms attached toan alkyl group having from p to q carbon atoms. In some embodiments,cycloalkylalkyl is C₃₋₇ cycloalkyl-C₁₋₃ alkyl, wherein the cycloalkylportion is monocyclic or bicyclic. Examples include cyclopropylmethyl,cyclobutylmethyl, cyclopentanemethyl, and cyclohexylmethyl.

The term “heterocycloalkyl”, employed alone or in combination with otherterms, refers to a non-aromatic ring or ring system, which mayoptionally contain one or more alkenylene groups as part of the ringstructure, which has at least one heteroatom ring member independentlyselected from nitrogen, sulfur, and oxygen. An “n-memberedheterocycloalkyl” wherein n is an integer, refers to a heteroaryl havingn ring-forming atoms. An “n-m membered heterocycloalkyl” wherein n and mare integers, refers to a heterocycloalkyl having from n to mring-forming atoms. The number of carbon atoms in the ring is fewer thanthe number of ring forming atoms by the number of heteroatoms. Thus, insome embodiments, an n-membered heterocycloalkyl may have n-1, n-2, n-3or n-4 ring carbon atoms and an n-m membered heterocycloalkyl may havefrom n-1, n-2, n-3 or n-4 ring carbon atoms to m-1, m-2, m-3 or m-4 ringcarbon atoms. In some embodiments, an n-m membered heterocycloalkyl mayhave from 1 to m-1 ring carbon atoms. In some embodiments, aheterocycloalkyl has 4-12 ring members, 4-10 ring members, 4-7 ringmembers or 4-6 ring members. Included in heterocycloalkyl groups aremonocyclic 4-, 5-, 6- and 7-membered heterocycloalkyl groups.Heterocycloalkyl groups can include mono- or bicyclic (e.g., having twofused or bridged rings) ring systems. In some embodiments, theheterocycloalkyl group is a monocyclic group having 1, 2 or 3heteroatoms independently selected from nitrogen, sulfur and oxygen.Ring-forming carbon atoms and heteroatoms of a heterocycloalkyl groupcan be optionally oxidized to form an oxo or sulfide group or otheroxidized linkage (e.g., C(O), S(O), C(S) or S(O)₂, N-oxide etc.) or anitrogen atom can be quaternized. The heterocycloalkyl group can beattached through a ring-forming carbon atom or a ring-formingheteroatom. In some embodiments, the heterocycloalkyl group contains 0to 3 double bonds. In some embodiments, the heterocycloalkyl groupcontains 0 to 2 double bonds. Also included in the definition ofheterocycloalkyl are moieties that have one or more aromatic rings fused(i.e., having a bond in common with) to the heterocycloalkyl ring, e.g.,benzo or thienyl derivatives of piperidine, morpholine, azepine, etc. Aheterocycloalkyl group containing a fused aromatic ring can be attachedthrough any ring-forming atom including a ring-forming atom of the fusedaromatic ring. Examples of heterocycloalkyl groups include azetidine,azepane, dihydrobenzofuran, dihydrofuran, dihydropyran, morpholine,3-oxa-9-azaspiro[5.5]undecane, 1-oxa-8-azaspiro[4.5]decane, piperidine,piperazine, pyran, pyrrolidine, quinuclidine, tetrahydrofuran,tetrahydropyran, 1,2,3,4-tetrahydroquinoline, tropane, andthiomorpholine.

As used herein, the term “heterocycloalkylalkyl,” employed alone or incombination with other terms, refers to a group of formula-alkylene-heterocycloalkyl. The term “n-membered heterocycloalkylalkyl”wherein n is an integer refers to a hereoarylalkylalkyl group in whichthe heterocycloalkyl is n-membered. The term “n-m membered-C_(p-q)-alkylwherein n, m, p and q are integers refers to heterocycloalkylalkyl groupin which the heterocycloalkyl is n to m membered and the alkyl has fromp to q carbon atoms. In some embodiments, heterocycloalkylalkyl is 4-10membered heterocycloalkyl-C₁₋₃ alkyl or C₁₋₉ heterocycloalkyl-C₁₋₃alkyl, wherein the heterocycloalkyl portion is monocyclic or bicyclicand has 1, 2, 3, 4 or 5 heteroatom ring members independently selectedfrom nitrogen, sulfur and oxygen. In some embodiments,heterocycloalkylalkyl is C₂₋₉ heterocycloalkyl-C₁₋₄ alkyl or C₂₋₉heterocycloalkyl-C₁₋₃ alkyl, wherein the heterocycloalkyl portion ismonocyclic or bicyclic and has 1, 2, 3, or 4 heteroatom ring membersindependently selected from nitrogen, sulfur and oxygen.

At certain places, the definitions or embodiments may refer to specificrings (e.g., an azetidine ring, a pyridine ring, etc.). Unless otherwiseindicated, these rings can be attached to any ring member provided thatthe valency of the atom is not exceeded. For example, an azetidine ringmay be attached at any position of the ring, whereas an azetidin-3-ylring is attached at the 3-position.

When any two groups or two instances of the same substituent group are“independently selected” from a list of alternatives, the groups may bethe same or different. For example, if R^(a) and R^(b) are independentlyselected from the group consisting of alkyl, fluoro, amino, andhydroxyalkyl, then a molecule with two R^(a) groups and two R^(b) groupscould have all groups be alkyl group (e.g., four different alkylgroups). Alternatively, the first R^(a) could be alkyl, the second R^(a)could be fluoro, the first R^(b) could be hydroxyalkyl, and the secondR^(b) could be amino (or any other substituents taken from the group).Alternatively, both R^(a) and the first R^(b) could be fluoro, while thesecond R^(b) could be alkyl (i.e., some pairs of substituent groups maybe the same, while other pairs may be different). Unless otherwiseindicated, if two or more groups having the same definition are present,but the definition provides for alternatives, it should be understoodthat each occurrence of the same group is independently selected fromthe possible alternatives. For example, if two or more R^(a) groups arepresent in a compound, and the definition of R^(a) provides that R^(a)can be A, B or C, then it should be understood that each R^(a) grouppresent in the compound is independently chosen from A, B and C, so thatthe R^(a) groups present in the compound can be the same or different.

The compounds described herein can be asymmetric (e.g., having one ormore stereocenters). All stereoisomers, such as enantiomers anddiastereomers, are intended unless otherwise indicated. Compoundsdescribed herein that contain asymmetrically substituted carbon atomscan be isolated in optically active or racemic forms. Methods on how toprepare optically active forms from optically inactive startingmaterials are known in the art, such as by resolution of racemicmixtures or by stereoselective synthesis. Many geometric isomers ofolefins, C═N double bonds and the like can also be present in thecompounds described herein, and all such stable isomers are contemplatedin the present invention. Cis and trans geometric isomers of thecompounds of the present invention are described and may be isolated asa mixture of isomers or as separated isomeric forms.

Resolution of racemic mixtures of compounds can be carried out by any ofnumerous methods known in the art. One method includes fractionalrecrystallization using a chiral resolving acid which is an opticallyactive, salt-forming organic acid. Suitable resolving agents forfractional recrystallization methods are, e.g., optically active acids,such as the D and L forms of tartaric acid, diacetyltartaric acid,dibenzoyltartaric acid, mandelic acid, malic acid, lactic acid or thevarious optically active camphorsulfonic acids such as β-camphorsulfonicacid. Other resolving agents suitable for fractional crystallizationmethods include stereoisomerically pure forms of α-methylbenzylamine(e.g., S and R forms, or diastereomerically pure forms),2-phenylglycinol, norephedrine, ephedrine, N-methylephedrine,cyclohexylethylamine, 1,2-diaminocyclohexane and the like.

Resolution of racemic mixtures can also be carried out by elution on acolumn packed with an optically active resolving agent (e.g.,dinitrobenzoylphenylglycine). Suitable elution solvent composition canbe determined by one skilled in the art.

In some embodiments, the compounds of the invention have the(R)-configuration. In other embodiments, the compounds have the(S)-configuration. In compounds with more than one chiral centers, eachof the chiral centers in the compound may be independently (R) or (S),unless otherwise indicated.

Compounds described herein may also include tautomeric forms. Tautomericforms result from the swapping of a single bond with an adjacent doublebond together with the concomitant migration of a proton. Tautomericforms include prototropic tautomers which are isomeric protonationstates having the same empirical formula and total charge. Exampleprototropic tautomers include ketone-enol pairs, amide-imidic acidpairs, lactam-lactim pairs, enamine-imine pairs, and annular forms wherea proton can occupy two or more positions of a heterocyclic system,e.g., 1H- and 3H-imidazole, 1H-, 2H- and 4H-1,2,4-triazole, 1H- and2H-isoindole and 1H- and 2H-pyrazole. Tautomeric forms can be inequilibrium or sterically locked into one form by appropriatesubstitution. The disclosure is intended to encompass all such tautomersof the compounds described.

Compounds described herein can also include all isotopes of atomsoccurring in the intermediates or final compounds. Isotopes includethose atoms having the same atomic number but different mass numbers.For example, isotopes of hydrogen include tritium and deuterium.

The term, “compound,” as used herein is meant to include allstereoisomers, geometric isomers, tautomers and isotopes of thestructures depicted.

Compounds described herein may include acidic and/or basic groups and becapable of forming salts. It should be understood that the presentdisclosure is intended to include all salts of compounds that arecapable of forming salts, whether or not the possible existence of saltsis expressly described, including both acid and base salts of acompound. Furthermore, when a compound is described that is a salt, itis understood that the disclosure of the compound is intended to includeall forms of the compound, including the free base or free acid, as wellas alternative salt forms thereof. The term “salt” refers to derivativesof the disclosed compounds wherein the parent compound is modified byconverting an existing acid or base moiety to its salt form. Examples ofsalts include, but are not limited to, mineral or organic acid salts ofbasic residues such as amines; alkali or organic salts of acidicresidues such as carboxylic acids; and the like. The terms “a saltthereof,” “salt thereof,” or “salts thereof” can be applied to anypreceding member of an associated Markush group. For example, a groupconsisting of A, B, C, and salts thereof would include within its scopeembodiments that were a salt of A, embodiments that were a salt of B,and embodiments that were a salt of C.

Salts of the compounds disclosed herein include pharmaceuticallyacceptable salts. The term “pharmaceutically acceptable salts” refers tonon-toxic salts of the parent compound formed, e.g., from non-toxicinorganic or organic acids. The pharmaceutically acceptable salts of thepresent invention can be synthesized from the parent compound whichcontains a basic or acidic moiety by conventional chemical methods.Generally, such salts can be prepared by reacting the free acid or baseforms of these compounds with a stoichiometric amount of the appropriatebase or acid in water or in an organic solvent, or in a mixture of thetwo; generally, non-aqueous media like ether, ethyl acetate, alcohols(e.g., methanol, ethanol, iso-propanol or butanol) or acetonitrile(MeCN) are preferred. Lists of suitable salts are found in Remington'sPharmaceutical Sciences, 17^(th)h Ed., (Mack Publishing Company, Easton,1985), p. 1418, Berge et al., J. Pharm. Sci., 1977, 66(1), 1-19 and inStahl et al., Handbook of Pharmaceutical Salts: Properties, Selection,and Use, (Wiley, 2002). In some embodiments, the compounds describedherein include the N-oxide forms. Additional information on suitablepharmaceutically acceptable salts can be found in Remington's,Pharmaceutical Sciences (current edition), Mack Publishing Co., Easton,Pa., which is incorporated herein by reference.

Compounds, and salts thereof, including pharmaceutically acceptablesalts, can be found together with other substances such as water andsolvents (e.g., hydrates and solvates) or can be isolated. When in thesolid state, the compounds described herein, and salts thereof may occurin various forms and may, e.g., take the form of solvates, includinghydrates. The compounds may be in any solid-state form, such as apolymorph or solvate, so unless clearly indicated otherwise, referenceto compounds and salts thereof should be understood as encompassing anysolid-state form of the compound.

In some embodiments, the compounds described herein or salts thereof,are substantially isolated. By “substantially isolated” is meant thatthe compound is at least partially or substantially separated from theenvironment in which it was formed or detected. Partial separation caninclude, e.g., a composition enriched in the compounds of the invention.Substantial separation can include compositions containing at leastabout 50%, at least about 60%, at least about 70%, at least about 80%,at least about 90%, at least about 95%, at least about 97%, or at leastabout 99% by weight of the compounds of the invention, or salt thereof.

c. Abbreviations

The following abbreviations may be used herein and, unless otherwisenoted, have the meanings indicated below: p (micro); ° C. (degreesCelsius); Ac (acetyl); ACN (acetonitrile); anhyd (anhydrous); aq(aqueous); atm (atmosphere(s)); Bn (benzyl); Boc (tert-butoxycarbonyl);Bu (butyl); calcd (calculated); Cbz (benzyloxycarbonyl); chrom.(chromatography); CPME (cyclopentyl methyl ether); CH₂Cl₂(dichloromethane); concd (concentrated); cone (concentration); DCC (N,N′-dicyclohexylcarbodiimide); DIAD (Diisopropyl azodicarboxylate); DIEA(N,N-diisopropylethylamine); DMAP (4-(N,N-dimethylamino)pyridine); DMF(dimethylformamide); DMSO (dimethylsulfoxide); EDC(N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide hydrochloride); equiv(equivalent); ES (electrospray); Et (ethyl); Et₂O (diethyl ether); g(gram(s)); h (hour(s)); HATU(N-[(Dimethylamino)-1H-1,2,3-triazolo-[4,5-b]pyridin-1-ylmethylene]-N-methylmethanaminiumhexafluorophosphate N-oxide); HBTU(O-(Benzotriazol-1-yl)-N,N,N′,N′-tetramethyl-O-(1H-benzotriazol-1-yl)uroniumhexafluorophosphate,); HPLC (high-performance liquid chromatography);HOBt (1-hydroxybenzotriazole hydrate); L (liter(s)); m (milli);m-(meta); M (molar); MeCN (acetonitrile); min (minute(s)); mL(milliliter); mol (mole; molecular (as in mol wt)); Ms(methanesulfonyl); MS (mass spectrometry); MW (molecular weight); NBS(N-bromosuccinimide); NCS (N-chlorosuccinimide); NIS(N-iodosuccinimide); NHS (N-hydroxysuccinimide); NMM(4-methylmorpholine); NMR (nuclear magnetic resonance); o-(ortho); obsd(observed); p-(para); Ph (phenyl); Phth (Phthalimide); ppt(precipitate); Pr (propyl); psi (pounds per square inch); temp(temperature); TFA (trifluoroacetic acid); THF (tetrahydrofuran); TPP(triphenylphosphine); and Tr (trityl). Other abbreviations may also beused and have the meanings that would be understood by the person havingskill in the art.

II. Compounds A. Compounds of Formula I-1

In certain aspects, the present disclosure provides a compound ofFormula (I-1):

or a salt thereof, wherein:

Cy^(1A) is unsubstituted or substituted C₆₋₁₀ aryl or unsubstituted orsubstituted 5-10 membered heteroaryl; wherein the ring atoms of the 5-10membered heteroaryl forming Cy^(1A) consist of carbon atoms and 1, 2, or3 heteroatoms selected from O, N and S; wherein the substituted C₆₋₁₀aryl or substituted 5-10 membered heteroaryl forming Cy^(1A) aresubstituted with 1, 2, 3, 4 or 5 substituents each independentlyselected from R^(Cy1A), halogen, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), C(═NOR^(a11))NR^(c11)R^(d11),C(═NOC(O)R^(b11))NR^(c11)R^(d11), C(═NR^(e11))NR^(c11)C(O)OR^(a11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo;

each R^(Cy1A) is independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl,C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl and4-10 membered heterocycloalkyl, wherein the ring atoms of the 5-10membered heteroaryl or 4-10-membered heterocycloalkyl forming R^(Cy1A)consist of carbon atoms and 1, 2, 3 or 4 heteroatoms selected from O, Nand S, wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl formingR^(Cy1A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, CN, OR^(a11),SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo, and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; R¹¹ is H or C₁₋₆ alkyl, C₆₋₁₀ aryl-C₁₋₆alkyl or 5-10 membered heteroaryl-C₁₋₆ alkyl, wherein the C₁₋₆ alkylforming R¹¹ is unsubstituted or substituted by 1, 2 or 3 substituentsindependently selected from halogen, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo, and wherein the C₆₋₁₀ aryl-C₁₋₆ alkyl or5-10 membered heteroaryl-C₁₋₆ alkyl forming R¹¹ is unsubstituted orsubstituted by 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo;

R¹² is H or C₁₋₆ alkyl; or

R¹¹ and R¹², together with the groups to which they are attached, form a4-6 membered heterocycloalkyl ring;

A¹¹ is CR¹³R¹⁵ or N;

each R¹³ is independently Cy^(1B), (CR^(13A)R^(13B))_(n3)Cy^(1B), (C₁₋₆alkylene)Cy^(1B), (C₂₋₆ alkenylene)Cy^(1B), (C₂₋₆ alkynylene)Cy^(1B) orOCy^(1B), wherein the C₁₋₆ alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylenecomponent of R¹³ is unsubstituted or substituted by 1, 2, 3, 4 or 5substituents each independently selected from the group consisting ofhalogen, CN, OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11),C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo;

each R¹⁴ is independently selected from H and C₁₋₆ alkyl;

R¹⁵ is selected from H, R¹³, C₁₋₆ alkyl and OH;

a pair of R¹⁴ groups attached to adjacent carbon atoms, or a pairing ofR¹⁴ and R¹⁵ groups attached to adjacent carbon atoms, may, independentlyof other occurrences of R¹⁴, together be replaced a bond connecting theadjacent carbon atoms to which the pair of R¹⁴ groups or pairing of R¹⁴and R¹⁵ groups is attached, such that the adjacent carbon atoms areconnected by a double bond; or

a pair of R¹⁴ groups attached to the same carbon atom, or a pairing ofR¹³ and R¹⁵ groups attached to the same carbon atom, may, independentlyof other occurrences of R¹⁴, and together with the carbon atom to whichthe pair of R¹⁴ groups or pairing of R¹³ and R¹⁵ groups is attachedtogether form a spiro-fused C₃₋₁₀ cycloalkyl or 4-10 memberedheterocycloalkyl ring, wherein the ring atoms of the 4-10 memberedheterocycloalkyl ring formed consist of carbon atoms and 1, 2, or 3heteroatoms selected from O, N and S, wherein the spiro-fused C₃₋₁₀cycloalkyl or 4-10 membered heterocycloalkyl ring formed is optionallyfurther substituted with 1, 2 or 3 substituents independently selectedfrom halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, haloalkyl, CN,OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11),OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), S(O)₂R^(b11),NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo; or

pairs of R¹⁴ groups attached to adjacent carbon atoms, or a pairing ofR¹⁴ and R¹⁵ groups attached to adjacent carbon atoms, may, independentlyof other occurrences of R¹⁴, together with the adjacent carbon atoms towhich the pair of R¹⁴ groups or pairing of R¹⁴ and R¹⁵ groups isattached, form a fused C₃₋₁₀ cycloalkyl or 4-10 memberedheterocycloalkyl ring, wherein the ring atoms of the 4-10 memberedheterocycloalkyl ring formed consist of carbon atoms and 1, 2, or 3heteroatoms selected from O, N and S, wherein the fused C₃₋₁₀ cycloalkylor 4-10 membered heterocycloalkyl ring formed is optionally furthersubstituted with 1, 2 or 3 substituents independently selected fromhalogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, haloalkyl, CN,OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11),OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; or

a grouping of four R¹⁴ groups attached to two adjacent carbon atoms, ora grouping of two R¹⁴, one R¹³ and one R¹⁵ groups attached to twoadjacent carbon atoms, may, independently of other occurrences of R¹⁴,together with the two adjacent carbon atoms to which the grouping offour R¹⁴ groups or grouping of two R¹⁴, one R¹³ and one R¹⁵ groups areattached, form a fused C₆₋₁₀ aryl or 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl or 4-10 membered heterocycloalkyl ring, wherein the ringatoms of the 5-10 membered heteroaryl or 4-10 membered heterocycloalkylring formed consist of carbon atoms and 1, 2, or 3 heteroatoms selectedfrom O, N and S, and wherein the fused C₆₋₁₀ aryl or 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl or 4-10 membered heterocycloalkyl ringformed is optionally further substituted with 1, 2 or 3 substituentsindependently selected from halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11),C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11),NR^(c11)R^(d11), NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11),NR^(c11)C(O)OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo;

n1 is 1 or 2;

n2 is 0, 1 or 2;

provided that the sum of n1 and n2 is 1, 2 or 3;

provided that if n1 is 1 or n2 is 0, then A¹¹ is CR¹³R¹⁵;

n3 is 0, 1 or 2;

each R^(13A) is independently H or C₁₋₆ alkyl;

each R^(13B) is independently H or C₁₋₆ alkyl; or

or R^(13A) and R^(13B) attached to the same carbon atom, independentlyof any other R^(13A) and R^(13B) groups, together may form —(CH₂)₂₋₅—,thereby forming a 3-6 membered cycloalkyl ring;

Cy^(1B) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(1B) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and

wherein the substituted C₆₋₁₀ aryl, substituted 5-10 memberedheteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(1B) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy1B), halogen, C₁₋₆haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11),C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), C(═NOR^(a11))NR^(c11)R^(d11),C(═NOC(O)R^(b11))NR^(c11)R^(d11), C(═NR^(e11))NR^(c11)C(O)OR^(a11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo;

wherein each R^(Cy1B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy1B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy1B) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a11),SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a)n, OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1B) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo;

R¹⁶ is H, Cy^(1C), C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl, whereinthe C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl forming R¹⁶ isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents selectedfrom the group consisting of Cy^(1C), halogen, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo, provided that no more than one of thesubstituents of R¹⁶ is Cy^(1C);

Cy^(1C) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(1C) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and

wherein the substituted C₆₋₁₀ aryl, substituted 5-10 memberedheteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(1C) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy1C), halogen, C₁₋₆haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11),C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), C(═NOR^(a11))NR^(c11)R^(d11),C(═NOC(O)R^(b11))NR^(c11)R^(d11), C(═NR^(e11))NR^(c11)C(O)OR^(a11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo;

wherein each R^(Cy1C) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy1C) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy1C) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a11),SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a)n, OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1C) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo;

R^(a11), R^(b11), R^(c11) and R^(d11) are each independently selectedfrom H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a11), R^(b11), R^(c11) and R^(d11) are each optionallysubstituted with 1, 2, 3, 4 or 5 substituents independently selectedfrom C₁₋₆ alkyl, halo, CN, OR^(a12), SR^(a12), C(O)R^(b12),C(O)NR^(c12)R^(d12), C(O)OR^(a12), OC(O)R^(b12), OC(O)NR^(c12)R^(d12),NR^(c12)R^(d12), NR^(c12)C(O)R^(b12), NR^(c12)C(O)NR^(c12)R^(d12),NR^(c12)C(O)OR^(a12), C(═NR^(e12))NR^(c12)R^(d12),NR^(c12)C(═NR^(e12))NR^(c12)R^(d12), S(O)R^(b12), S(O)NR^(c12)R^(d12),S(O)₂R^(b12), NR^(c12)S(O)₂R^(b12), S(O)₂NR^(c12)R^(d12) and oxo;

or R^(c11) and R^(d11) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each optionallysubstituted with 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, halo, CN, OR^(a12), SR^(a12), C(O)R^(b12), C(O)NR^(c12)R^(d12),C(O)OR^(a12), OC(O)R^(b12), OC(O)NR^(c12)R^(d12), NR^(c12)R^(d12),NR^(c12)C(O)R^(b12), NR^(c12)C(O)NR^(c12)R^(d12), NR^(c12)C(O)OR^(a12),C(═NR^(e12))NR^(c12)R^(d12), NR^(c12)C(═NR^(e12))NR^(c12)R^(d12),S(O)R^(b12), S(O)NR^(c12)R^(d12), S(O)₂R^(b12), NR^(c12)S(O)₂R^(b12),S(O)₂NR^(c12)R^(d12) and oxo; R^(a12), R^(b12), R^(c12) and R^(d12) areeach independently selected from H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 membered heteroaryl,4-7 membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6 memberedheteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7 memberedheterocycloalkyl-C₁₋₃ alkyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl,C₂₋₆ alkenyl, C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 memberedheteroaryl, 4-7 membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6membered heteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7membered heterocycloalkyl-C₁₋₃ alkyl forming R^(a12), R^(b12), R^(c12)and R^(d12) are each optionally substituted with 1, 2 or 3 substituentsindependently selected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxyand oxo;

or R^(c12) and R^(d12) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each of which isunsubstituted or substituted with 1, 2 or 3 substituents independentlyselected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo; and

R^(e11) and R^(e12) are each, independently, H, CN or NO₂.

In some embodiments, the compound is of Formula (I-2):

In some embodiments, Cy is unsubstituted or substituted aryl.

In some embodiments, Cy^(1A) is unsubstituted or substituted phenyl.

In some embodiments, Cy^(1A) is substituted phenyl.

In some embodiments, Cy^(1A) is substituted with at least one OR^(a11)or at least one C(═NR^(e11))NR^(c11)R^(d11),C(═NOR^(a11))NR^(c11)R^(d11), C(═NOC(O)R^(b11))NR^(c11)R^(d11), orC(═NR^(e11))NR^(c11)C(O)OR^(a11).

In some embodiments, Cy^(1A) is substituted with at least one OR^(a11)and by at least one additional substituent selected from the groupconsisting of C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(1A) is substituted with at least one OH and byat least one additional substituent selected from the group consistingof C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(1A) is substituted with at least oneC(═NR^(e11))NR^(c11)R^(d11), C(═NOR^(a11))NR^(c11)R^(d11),C(═NOC(O)R^(b11))NR^(c11)R^(d11), C(═NR^(e11))NR^(c11)C(O)OR^(a11),preferably in the 4-position.

In some embodiments, Cy^(1A) is substituted with at least oneC(═NR^(e11))NR^(c11)R^(d11), preferably in the 4-position.

In some embodiments, Cy^(1A) is substituted with at least one C(═NH)NH₂,preferably in the 4-position.

In some embodiments, Cy^(1A) is of any one of the following formulae:

In some embodiments, in the formula defining Cy^(1A), each R^(Cy1A) isindependently C₁₋₆ alkyl, such as methyl, or halogen, such as Cl or Br,or amino.

In some embodiments, Cy^(1A) is of any one of the following formulae:

In some embodiments, in the formula defining Cy^(1A), R^(a11) is C₁₋₆alkyl, such as methyl, R^(b11) is C₁₋₆ alkyl, such as methyl, R^(b11) isC₁₋₆ haloalkyl, such as trifluoromethyl, and R^(c11) is alkyl such asmethyl.

In some embodiments, Cy^(1A) is unsubstituted or substituted heteroaryl.

In some embodiments, Cy^(1A) is unsubstituted or substitutedpyridin-3-yl, 1H-pyrrolo[2,3-b]pyridine-5-yl, or1H-benzo[d]imidazol-6-yl.

In some embodiments, Cy^(1A) is of any one of the following formulae:

In some embodiments, each R^(Cy1A) in the formula defining Cy^(1A) isindependently C₁₋₆ alkyl, such as methyl or ethyl, preferably methyl, orhalogen such as F, Cl or Br, preferably Cl, or amino.

In some embodiments, each R^(Cy1A) attached to nitrogen in the formuladefining Cy^(1A) is C₁₋₆ alkyl, such as methyl or ethyl.

In some embodiments, R¹¹ is C₁₋₆ alkyl.

In some embodiments, R¹¹ is methyl.

In some embodiments, R¹¹ is H.

In some embodiments, R¹² is H.

In some embodiments, R¹² is C₁₋₆ alkyl, such as methyl or ethyl,preferably methyl.

In some embodiments, R¹¹ and R¹², together with the groups to which theyare attached, form a 4-6 membered heterocycloalkyl ring.

In some embodiments, n1 is 1.

In some embodiments, n1 is 2.

In some embodiments, n2 is 0.

In some embodiments, n2 is 1.

In some embodiments, n2 is 2.

In some embodiments, the compound is according to any of the followingFormulae (I-1a) to (I-1f) and (I-2a) to (I-2r):

In some embodiments, the compound is according to any of the followingFormulae (I-1g) to (I-1o) and (I-2aa) to (I-2az):

In some embodiments, the compound is according to any of the followingFormulae (I-3) to (I-9):

In some embodiments, the compound is according to any of the followingFormulae (I-3a) to (1-3k):

In some embodiments, the compound is according to any of the followingFormulae (I-4a) to (1-4bf):

In some embodiments, the compound is according to any of the followingFormulae (I-5a) to (I-5u):

In some embodiments, the compound is according to any of the followingFormulae (I-6a) to (I-6cw):

In some embodiments, the compound is according to any of the followingFormulae (I-7a) to (I-7co):

In some embodiments, the compound is according to any of the followingFormulae (I-8a) to (I-8z):

In some embodiments, the compound is according to any of the followingFormulae (I-9a) to (I-9z):

In some embodiments, R¹³ is Cy^(1B).

In some embodiments, R¹³ is (C₁₋₆ alkylene)Cy^(1B), (C₂₋₆alkenylene)Cy^(1B), or (C₂₋₆ alkynylene)Cy^(1B). In some embodiments,the C₁₋₆ alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R¹³is unsubstituted.

In some embodiments, R¹³ is (CR^(13A)R^(13B))_(n3)Cy^(1B).

In some embodiments, each R^(13A) is H.

In some embodiments, each R^(13B) is H.

In some embodiments, n3 is 0.

In some embodiments, n3 is 1.

In some embodiments, n3 is 2.

In some embodiments, R¹³ is (CH₂)₀₋₂Cy^(1B).

In some embodiments, R¹³ is CH₂Cy^(1B).

In some embodiments, R¹³ is CH₂CH₂Cy^(1B).

In some embodiments, R¹³ is OCy^(1B).

In some embodiments, Cy^(1B) is unsubstituted C₆₋₁₀ aryl.

In some embodiments, Cy^(1B) is unsubstituted phenyl.

In some embodiments, Cy^(1B) is unsubstituted naphthyl, such as1-naphthyl or 2-naphthyl.

In some embodiments, Cy^(1B) unsubstituted 5-10 membered heteroaryl.

In some embodiments, Cy^(1B) is unsubstituted pyridyl, such asunsubstituted 2-, 3-, or 4-pyridyl or unsubstituted quinolyl, such asunsubstituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl.

In some embodiments, Cy^(1B) is substituted C₆₋₁₀ aryl.

In some embodiments, Cy^(1B) is substituted phenyl.

In some embodiments, Cy^(1B) is a biphenylyl (i.e., phenyl substitutedby phenyl), such as 2-, 3-, or 4-biphenylyl.

In some embodiments, Cy^(1B) is substituted naphthyl, such as 1-naphthylor 2-naphthyl.

In some embodiments, Cy^(1B) substituted 5-10 membered heteroaryl.

In some embodiments, Cy^(1B) is substituted pyridyl, such as substituted2-, 3-, or 4-pyridyl or substituted quinolyl, such as substituted 2-,3-, 4-, 5-, 6-, 7-, or 8-quinolyl.

In some embodiments, Cy^(1B) is substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy1B), halogen, andC₁₋₆ haloalkyl; wherein each R^(Cy1B) is independently selected fromC₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl and C₆₋₁₀ aryl or 5-10 memberedheteroaryl, wherein each C₆₋₁₀ aryl or 5-10 membered heteroaryl formingR^(Cy1B) is unsubstituted or substituted with 1, 2 or 3 substituentsindependently selected from halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, and haloalkyl.

In some embodiments, R¹³ is selected from groups of the followingformulae:

In some embodiments, R^(Cy1B) in the formula representing R¹³ is C₁₋₆alkyl, such as methyl or ethyl, preferably methyl, or halogen, such asfluorine or chlorine, preferably fluorine.

In some embodiments, R^(Cy1B) in the formula representing R¹³ is C₁₋₆alkyl, such as methyl or ethyl, preferably methyl.

In some embodiments, R^(Cy1B) in the formula representing R¹³ ishalogen, such as fluorine or chlorine, preferably fluorine.

In some embodiments, no more than one R¹⁴ is other than hydrogen.

In some embodiments, no more than one R¹⁴ is other than hydrogen and oneR¹⁴ is C₁₋₆ alkyl, such as methyl.

In some embodiments, each R¹⁴ is hydrogen.

In some embodiments, A¹¹ is N.

In some embodiments, R¹⁵ is hydrogen.

In some embodiments, R¹⁵ is C₁₋₆ alkyl such as methyl.

In some embodiments, R¹⁵ is hydroxyl.

In some embodiments, R¹⁶ is hydrogen.

In some embodiments, R¹⁶ is unsubstituted or substituted C₁₋₆ alkyl,C₂₋₆ alkenyl, or C₂₋₆ alkynyl.

In some embodiments, R¹⁶ is unsubstituted C₁₋₆ alkyl such as methyl.

In some embodiments, R¹⁶ is substituted C₁₋₆ alkyl.

In some embodiments, the substituted C₁₋₆ alkyl forming R¹⁶ issubstituted by 1, 2, 3, 4 or 5, such as 1, 2, or 3, or, preferably 1,substituents selected from the group consisting of halogen, CN,C(O)NR^(c11)R^(d11) and C(O)OR^(a11).

In some embodiments, R¹⁶ is (CH₂)₁₋₆C(O)OR^(a11).

In some embodiments, the R^(a11) defining R¹⁶ is H or C₁₋₆ alkyl such asmethyl.

In some embodiments, the R^(a11) defining R¹⁶ is H.

In some embodiments, R^(a11), R^(b11), R^(c11) and R^(d11), R^(a12),R^(b12), R^(c12) and R^(d12) are each independently selected from H andC₁₋₆ alkyl.

In some embodiments, each R^(e11) and each R^(e12) is H.

In some embodiments, the compounds of Formula (I-1), and embodimentsthereof, can be in the form of a salt such as a pharmaceuticallyacceptable salt.

The compounds of Formula (I-1), and embodiments thereof, are useful asinhibitors of MASP-2 and for therapeutic use. The compounds of Formula(I-1), and embodiments thereof, are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (I-1), or anembodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (I-1) or an embodiment thereofis provided in the form of a pharmaceutical composition comprising thecompound or a salt thereof, such as a pharmaceutically acceptable salt,and at least one pharmaceutically acceptable carrier or excipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (I-1) set forth in the Examples, including thecompounds listed in Table 31, e.g., the compounds with selectivity forMASP-2 over thrombin). In certain aspects, one or more of the variablesdefining the compounds of Formula (I) (such as Cy^(1A); R^(Cy1A); R¹¹;R¹²; A¹¹; R¹³; R¹⁴; R¹⁵; n1; n2; n3; R^(13A); R^(13B); Cy^(1B); R¹⁶;R^(16A); R^(16B); Cy^(1C); R^(Cy1C); R^(a11), R^(b11), R^(c11); R^(d11);R^(e11), R^(a12), R^(b12), R^(c12); R^(d12); and R^(e12)) is selectedfrom the corresponding substituents in the compounds of Formula (I-1) inthe Examples including the compounds listed in Table 31, preferably,those of the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

B. Compounds of Formula IIA and IIB

In certain aspects, the present disclosure provides a compound ofFormula (IIA) and (IIB):

or a salt thereof, wherein:

Cy^(2A) is unsubstituted or substituted C₆₋₁₀ aryl or unsubstituted orsubstituted 5-10 membered heteroaryl; wherein the ring atoms of the 5-10membered heteroaryl forming Cy^(2A) consist of carbon atoms and 1, 2, or3 heteroatoms selected from O, N and S; wherein the substituted C₆₋₁₀aryl or substituted 5-10 membered heteroaryl forming Cy^(2A) aresubstituted with 1, 2, 3, 4 or 5 substituents each independentlyselected from R^(Cy2A), halogen, C₁₋₆ haloalkyl, CN, OR²¹, SR^(a21),C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21), OC(O)R^(b21),OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21), NR^(c21)C(O)R^(b21),NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), C(═NOR^(a21))NR^(c21)R^(d21),C(═NOC(O)R^(b21))NR^(c21)R^(d21), C(═NR^(e21))NR^(c21)C(O)OR^(a21),NR^(c21)C(═NR^(e21))NR^(c21)R^(d21), S(O)R^(b21), S(O)NR^(c21)R^(d21),S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21), S(O)₂NR^(c21)R^(d21) and oxo;

each R^(Cy2A) is independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl,C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl and4-10 membered heterocycloalkyl, wherein the ring atoms of the 5-10membered heteroaryl or 4-10-membered heterocycloalkyl forming R^(Cy2A)consist of carbon atoms and 1, 2, 3 or 4 heteroatoms selected from O, Nand S, wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl formingR^(Cy2A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, CN, OR^(a21),SR^(a21), C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21), OC(O)R^(b21),OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21), NR^(c21)C(O)R^(b21),NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(d21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(d21) and oxo, and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy2A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a21), SR^(a21),C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21), —OC(O)R^(b21),OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21), NR^(c21)C(O)R^(b21),NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(d21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(d21) and oxo;

R²¹ is H or C₁₋₆ alkyl, C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 memberedheteroaryl-C₁₋₆ alkyl, wherein the C₁₋₆ alkyl forming R²¹ isunsubstituted or substituted by 1, 2 or 3 substituents independentlyselected from halogen, CN, OR^(a21), SR^(a21), C(O)R^(b21),C(O)NR^(c21)R^(d21), C(O)OR^(a21), OC(O)R^(b21), OC(O)NR^(c21)R^(d21),NR^(c21)R^(d21), NR^(c21)C(O)R^(b21), NR^(c21)C(O)NR^(c21)R^(d21),NR^(c21)C(O)OR^(a21), C(═NR^(e21))NR^(c21)R^(d21),NR^(c21)C(═NR^(e21))NR^(c21)R^(d21), S(O)R^(b21), S(O)NR^(c21)R^(a21)S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21), S(O)₂NR^(c21)R^(d21) and oxo, andwherein the C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 membered heteroaryl-C₁₋₆ alkylforming R²¹ is unsubstituted or substituted by 1, 2 or 3 substituentsindependently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆haloalkyl, CN, OR^(a21), SR^(a21), C(O)R^(b21), C(O)NR^(c21)R^(d21),C(O)OR^(a21), OC(O)R^(b21), OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21),NR^(c21)C(O)R^(b21), NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(d21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(d21) and oxo;

R²² is H or C₁₋₆ alkyl; or

R²¹ and R²², together with the groups to which they are attached, form a4-6 membered heterocycloalkyl ring;

A²³ is N or NR²³;

A²⁴ is CR²⁴; N or NR²⁴;

A²⁶ is CR²⁶ or S;

provided that

A²³, A²⁴ and A²⁶ in Formula (HA) are selected such that the ringcomprising A²³, A²⁴ and A²⁶ is a heteroaryl ring and the symbol

represents an aromatic ring (normalized) bond;

R²³ is H or C₁₋₆ alkyl;

R²⁴ is H; C₁₋₆ alkyl or phenyl;

R²⁵ is Cy^(2B), (CR^(25A)R^(25B))_(n25)Cy^(2B), (C₁₋₆ alkylene)Cy^(2B),(C₂₋₆ alkenylene)Cy^(2B), or (C₂₋₆ alkynylene)Cy^(2B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R²⁵ isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents eachindependently selected from the group consisting of halogen, CN,OR^(a21), SR²¹, C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21),OC(O)R^(b21), OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21),NR^(c21)C(O)R^(b21), NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(a21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(a21) and oxo;

R²⁶ is H or C₁₋₆ alkyl;

each R^(25A) is H or C₁₋₆ alkyl;

each R^(25B) is H or C₁₋₆ alkyl;

n25 is 0, 1 or 2;

Cy^(2B) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(2B) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and

wherein the substituted C₆₋₁₀ aryl, substituted 5-10 memberedheteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(2B) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy2B), halogen, C₁₋₆haloalkyl, CN, OR²¹, SR^(a21), C(O)R^(b21), C(O)NR^(c21)R^(d21),C(O)OR^(a21), OC(O)R^(b21), OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21),NR^(c21)C(O)R^(b21), NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), C(═NOR^(a21))NR^(c21)R^(d21),C(═NOC(O)R^(b21))NR^(c21)R^(d21), C(═NR^(e21))NR^(c21)C(O)OR^(a21),NR^(c21)C(═NR^(e21))NR^(c21)R^(d21), S(O)R^(b21), S(O)NR^(c21)R^(d21),S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21), S(O)₂NR^(c21)R^(a21) and oxo;

wherein each R^(Cy2B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy2B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy2B) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a21),SR²¹, C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21), OC(O)R^(b21),OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21), NR^(c21)C(O)R^(b21),NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(d21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(d21) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy2B) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a1), SR^(a21),C(O)R^(b21), C(O)NR^(c21)R^(d21), C(O)OR^(a21), OC(O)R^(b21),OC(O)NR^(c21)R^(d21), NR^(c21)R^(d21), NR^(c21)C(O)R^(b21),NR^(c21)C(O)NR^(c21)R^(d21), NR^(c21)C(O)OR^(a21),C(═NR^(e21))NR^(c21)R^(d21), NR^(c21)C(═NR^(e21))NR^(c21)R^(d21),S(O)R^(b21), S(O)NR^(c21)R^(d21), S(O)₂R^(b21), NR^(c21)S(O)₂R^(b21),S(O)₂NR^(c21)R^(d21) and oxo;

R^(a21), R^(b21), R^(c21) and R^(d21) are each independently selectedfrom H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a21), R^(b21), R^(c21) and R^(d21) are each optionallysubstituted with 1, 2, 3, 4 or 5 substituents independently selectedfrom C₁₋₆ alkyl, halo, CN, OR²², SR^(a22), C(O)R^(b22),C(O)NR^(c22)R^(d22), C(O)OR²², OC(O)R^(b22), OC(O)NR^(c22)R^(d22),NR^(c22)R^(d22), NR^(c22)C(O)R^(b22), NR^(c22)C(O)NR^(c22)R^(d22),NR^(c22)C(O)OR^(a22), C(═NR^(e22))NR^(c22)R^(d22),NR^(c22)C(═NR^(e22))NR^(c22)R^(d22), S(O)R^(b22), S(O)NR^(c22)R^(d22),S(O)₂R^(b22), NR^(c22)S(O)₂R^(b22), S(O)₂NR^(c22)R^(d22) and oxo;

or R^(c21) and R^(d21) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each optionallysubstituted with 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, halo, CN, OR²², SR²², C(O)R^(b22), C(O)NR^(c22)R^(d22), C(O)OR²²,OC(O)R^(b22), OC(O)NR^(c22)R^(d22), NR^(c22)R^(d22),NR^(c22)C(O)R^(b22), NR^(c22)C(O)NR^(c22)R^(d22), NR^(c22)C(O)OR^(a22),C(═NR^(e22))NR^(c22)R^(d22), NR^(c22)C(═NR^(e22))NR^(c22)R^(d22),S(O)R^(b22), S(O)NR^(c22)R^(d22) S(O)₂R^(b22), NR^(c22)S(O)₂R^(b22),S(O)₂NR^(c22)R^(d22) and oxo;

R^(a22), R^(b22), R^(c22) and R^(d22) are each independently selectedfrom H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, phenyl,C₃₋₇ cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl,phenyl-C₁₋₃ alkyl, 5-6 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-7 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,phenyl, C₃₋₇ cycloalkyl, 5-6 membered heteroaryl, 4-7 memberedheterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6 membered heteroaryl-C₁₋₃ alkyl,C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a22), R^(b22), R^(c22) and R^(d22) are each optionallysubstituted with 1, 2 or 3 substituents independently selected from OH,CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo;

or R^(c22) and R^(d22) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each of which isunsubstituted or substituted with 1, 2 or 3 substituents independentlyselected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo; and

R^(e21) and R^(e22) are each, independently, H, CN or NO₂.

In some embodiments, Cy^(2A) is unsubstituted or substituted aryl.

In some embodiments, Cy^(2A) is unsubstituted or substituted phenyl.

In some embodiments, Cy^(2A) is substituted phenyl.

In some embodiments, Cy^(2A) is substituted with at least one OR²¹ or atleast one C(═NR^(e21))NR^(c21)R^(d21), C(═NOR^(a21))NR^(c21)R^(d21),C(═NOC(O)R^(b21))NR^(c21)R^(d21), or C(═NR^(e21))NR^(c21)C(O)OR^(a21).

In some embodiments, Cy^(2A) is substituted with at least one OR²¹ andby at least one additional substituent selected from the groupconsisting of C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(2A) is substituted with at least one OH and byat least one additional substituent selected from the group consistingof C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(2A) is substituted with at least oneC(═NR^(e21))NR^(c21)R^(d21), C(═NOR^(a21))NR^(c21)R^(d21),C(═NOC(O)R^(b21))NR^(c21)R^(d21), C(═NR^(e21))NR^(c21)C(O)OR^(a21),preferably in the 4-position.

In some embodiments, Cy^(2A) is substituted with at least oneC(═NR^(e21))NR^(c21)R^(d21), preferably in the 4-position.

In some embodiments, Cy^(2A) is substituted with at least one C(═NH)NH₂,preferably in the 4-position.

In some embodiments, Cy^(2A) is of any one of the following formulae:

In some embodiments, in the formula defining Cy^(2A), each R^(Cy2A) isindependently C₁₋₆ alkyl, such as methyl, or halogen, such as Cl or Br,or amino.

In some embodiments, Cy^(2A) is of any one of the following formulae:

In some embodiments, R²¹ is C₁₋₆ alkyl and R^(b21) is C₁₋₆ alkyl.

In some embodiments, Cy^(2A) is unsubstituted or substituted heteroaryl,such as pyridin-3-yl, 1H-pyrrolo[2,3-b]pyridine-5-yl, or1H-benzo[d]imidazol-6-yl.

In some embodiments, Cy^(2A) is of any one of the following formulae:

In some embodiments, each R^(Cy2A) in the formula defining Cy^(2A) isindependently C₁₋₆ alkyl, such as methyl or ethyl, preferably methyl, orhalogen such as F, Cl or Br, preferably Cl.

In some embodiments, each R^(Cy2A) attached to nitrogen in the formuladefining Cy^(2A) is C₁₋₆ alkyl, such as methyl or ethyl.

In some embodiments, R²¹ is C₁₋₆ alkyl.

In some embodiments, R²¹ is methyl.

In some embodiments, R²¹ is H.

In some embodiments, R²² is H.

In some embodiments, R²² is C₁₋₆ alkyl.

In some embodiments, R²² is methyl.

In some embodiments, R²¹ and R²², together with the groups to which theyare attached, form a 4-6 membered heterocycloalkyl ring.

In some embodiments, the compound is of Formula (IIA).

In some embodiments, the compound is according to any of the followingFormulae (IIA-1a) or (IIA-1b):

In some embodiments, the compound is according to any of the followingFormulae (IIA-2) to (IIA-5):

In some embodiments, the compound is according to any of the followingFormulae (IIA-2a) to (IIA-5b):

In some embodiments, the compound is of Formula (IIB).

In some embodiments, the compound is according to any of the followingFormulae (IIB-1a) or (IIB-1b):

In some embodiments, R²³ is H.

In some embodiments, R²³ is C₁₋₆ alkyl.

In some embodiments, R²⁴ is H.

In some embodiments, R²⁴ is C₁₋₆ alkyl.

In some embodiments, R²⁴ is phenyl.

In some embodiments, R²⁵ is Cy^(2B).

In some embodiments, R²⁵ is (C₁₋₆ alkylene)Cy^(2B), (C₂₋₆alkenylene)Cy^(2B), or (C₂₋₆ alkynylene)Cy^(2B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R²⁵ isunsubstituted or substituted.

In some embodiments, R²⁵ is (C₁₋₆ alkylene)Cy^(2B), (C₂₋₆alkenylene)Cy^(2B), or (C₂₋₆ alkynylene)Cy^(2B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R²⁵ isunsubstituted.

In some embodiments, R²⁵ is (CR^(25A)R^(25B))_(n25)Cy^(2B).

In some embodiments, each R^(25A) is H.

In some embodiments, each R^(25B) is H.

In some embodiments, n25 is 0.

In some embodiments, n25 is 1.

In some embodiments, n25 is 2.

In some embodiments, R²⁵ is CH₂Cy^(2B).

In some embodiments, R²⁵ is CH₂CH₂Cy^(2B).

In some embodiments, Cy^(2B) is unsubstituted C₆₋₁₀ aryl.

In some embodiments, Cy^(2B) is unsubstituted phenyl.

In some embodiments, Cy^(2B) is unsubstituted naphthyl, such as1-naphthyl or 2-naphthyl.

In some embodiments, Cy^(2B) unsubstituted 5-10 membered heteroaryl.

In some embodiments, Cy^(2B) is unsubstituted pyridyl, such asunsubstituted 2-, 3-, or 4-pyridyl or unsubstituted quinolyl, such asunsubstituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl.

In some embodiments, Cy^(2B) is substituted C₆₋₁₀ aryl.

In some embodiments, Cy^(2B) is substituted phenyl.

In some embodiments, Cy^(2B) is a biphenylyl (i.e., phenyl substitutedby phenyl), such as 2-, 3-, or 4-biphenylyl.

In some embodiments, Cy^(2B) is substituted naphthyl, such as 1-naphthylor 2-naphthyl.

In some embodiments, Cy^(2B) is substituted 5-10 membered heteroaryl.

In some embodiments, Cy^(2B) is substituted pyridyl, such as substituted2-, 3-, or 4-pyridyl or substituted quinolyl, such as substituted 2-,3-, 4-, 5-, 6-, 7-, or 8-quinolyl.

In some embodiments, Cy^(2B) is substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy2B), halogen, andC₁₋₆ haloalkyl; wherein each R^(Cy2B) is independently selected fromC₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl and C₆₋₁₀ aryl or 5-10 memberedheteroaryl, wherein each C₆₋₁₀ aryl or 5-10 membered heteroaryl formingR^(Cy2B) is unsubstituted or substituted with 1, 2 or 3 substituentsindependently selected from halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, and haloalkyl.

In some embodiments, R²⁵ is selected from groups of the followingformulae:

In some embodiments, R^(Cy2B) in the formula representing R²⁵ is C₁₋₆alkyl, such as methyl or ethyl, preferably methyl, or halogen, such asfluorine or chlorine, preferably fluorine.

In some embodiments, R^(Cy2B) in the formula representing R²⁵ is C₁₋₆alkyl, such as methyl or ethyl, preferably methyl.

In some embodiments, R^(Cy2B) in the formula representing R²⁵ ishalogen, such as fluorine or chlorine, preferably fluorine.

In some embodiments, R^(a21), R^(b21), R^(c21), R^(a21), R^(a22),R^(b22), R^(c22), R^(a22) are each independently selected from H, C₁₋₆alkyl.

In some embodiments, each R^(e21) and each R^(e22) is H.

The compounds of Formula (IIA) and (IIB), and embodiments thereof, areuseful as inhibitors of MASP-2 and for therapeutic use.

In some embodiments, the compounds of Formula (IIA) and (IIB), andembodiments thereof, can be in the form of a salt such as apharmaceutically acceptable salt.

The compounds of Formula (IIA) and (IIB), and embodiments thereof, areuseful as inhibitors of MASP-2 and for therapeutic use. The compounds ofFormula (IIA) and (IIB), and embodiments thereof, are useful in thetreatment of MASP-2-associated diseases and disorders, and in themanufacture of medicaments for treating MASP-2-associated diseases anddisorders. The present disclosure also provides methods of treating aMASP-2-associated disease and disorder comprising administering to apatient a therapeutically effective amount of a compound of Formula(IIA) or (IIB), or an embodiment thereof, optionally in the form of asalt.

In some embodiments the compound Formula (IIA) or (IIB) or an embodimentthereof is provided in the form of a pharmaceutical compositioncomprising the compound or a salt thereof, such as a pharmaceuticallyacceptable salt, and at least one pharmaceutically acceptable carrier orexcipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (IIA) and (IIB) set forth in the Examples includingthe compounds listed in Table 31, e.g., the compounds with selectivityfor MASP-2 over thrombin. In certain aspects, one or more of thevariables defining the compounds of Formula (IIA) and (IIB) (such asCy^(2A), R^(Cy2A), Cy^(2B), R^(Cy2B), A²³, A²⁴, A²⁶, R²¹, R²², R²³, R²⁴,R²⁵, R²⁶, n25, R^(a21), R^(b21), R^(c21), R^(d21), R^(e21), R^(a22),R^(b22), R^(c22), R^(d22) and R^(e22)) is selected from thecorresponding substituents in the compounds of Formula (IIA) and (IIB)in the Examples, including the compounds listed in Table 31, preferably,those of the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

C. Compounds of Formula III

In certain aspects, the present disclosure provides a compound ofFormula (III).

or a salt thereof, for use in treating a MASP-2-associated disease ordisorder, wherein:

Cy^(3A) is unsubstituted or substituted C₆₋₁₀ aryl or unsubstituted orsubstituted 5-10 membered heteroaryl; wherein the ring atoms of the 5-10membered heteroaryl forming Cy^(3A) consist of carbon atoms and 1, 2, or3 heteroatoms selected from O, N and S; wherein the substituted C₆₋₁₀aryl or substituted 5-10 membered heteroaryl forming Cy^(3A) aresubstituted with 1, 2, 3, 4 or 5 substituents each independentlyselected from R^(Cy3A), halogen, C₁₋₆ haloalkyl, CN, OR^(a31), SR^(a31),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), C(═NOR^(a31))NR^(c31)R^(d31),C(═NOC(O)R^(b31))NR^(c31)R^(d31), C(═NR^(e31))NR^(c31)C(O)OR^(a31),NR^(c31)C(═NR^(e31))NR^(c31)R^(d31), S(O)R^(b31), S(O)NR^(c31)R^(d31),S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31), S(O)₂NR^(c31)R^(d31) and oxo;

each R^(Cy3A) is independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl,C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl and4-10 membered heterocycloalkyl, wherein the ring atoms of the 5-10membered heteroaryl or 4-10-membered heterocycloalkyl forming R^(Cy3A)consist of carbon atoms and 1, 2, 3 or 4 heteroatoms selected from O, Nand S, wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl formingR^(Cy3A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, CN, OR^(a31),SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo, and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy3A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a31), SR^(a31),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo;

R³¹ is H or C₁₋₆ alkyl, C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 memberedheteroaryl-C₁₋₆ alkyl, wherein the C₁₋₆ alkyl forming R³¹ isunsubstituted or substituted by 1, 2 or 3 substituents independentlyselected from halogen, CN, OR^(a31), SR^(a31), C(O)R^(b31),C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31), OC(O)NR^(c31)R^(d31),NR^(c31)R^(d31), NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(d31),NR^(c31)C(O)OR^(a31), C(═NR^(e31))NR^(c31)R^(d31),NR^(c31)C(═NR^(e31))NR^(c31)R^(d31), S(O)R^(b31), S(O)NR^(c31)R^(d31),S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31), S(O)₂NR^(c31)R^(d31) and oxo, andwherein the C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 membered heteroaryl-C₁₋₆ alkylforming R³¹ is unsubstituted or substituted by 1, 2 or 3 substituentsindependently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆haloalkyl, CN, OR^(a31), SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31),C(O)OR^(a31), OC(O)R^(b31), OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31),NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo;

R³² is H or C₁₋₆ alkyl; or

R³¹ and R³², together with the groups to which they are attached, form a4-6 membered heterocycloalkyl ring;

R³³ is Cy^(3B), (CR^(33A)R^(33B))_(n33)Cy^(3B), (C₁₋₆ alkylene)Cy^(3B),(C₂₋₆ alkenylene)Cy^(3B), or (C₂₋₆ alkynylene)Cy^(3B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R³⁵ isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents eachindependently selected from the group consisting of halogen, CN,OR^(a31), SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31),OC(O)R^(b31), OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31),NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo;

each R^(33A) is independently H or C₁₋₆ alkyl;

each R^(33B) is independently H or C₁₋₆ alkyl; or

or R^(33A) and R^(33B) attached to the same carbon atom, independentlyof any other R^(33A) and R^(33B) groups, together may form —(CH₂)₂₋₅—,thereby forming a 3-6 membered cycloalkyl ring;

n33 is 0, 1, 2 or 3;

Cy^(3B) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(3B) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and

wherein the substituted C₆₋₁₀ aryl, substituted 5-10 memberedheteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(3B) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy3B), halogen, C₁₋₆haloalkyl, CN, OR^(a31), SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31),C(O)OR^(a31), OC(O)R^(b31), OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31),NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(c31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), C(═NOR^(a31))NR^(c31)R^(d31),C(═NOC(O)R^(b31))NR^(c31)R^(d31), C(═NR^(e31))NR^(c31)C(O)OR^(a31),NR^(c31)C(═NR^(e31))NR^(c31)R^(d31), S(O)R^(b31), S(O)NR^(c31)R^(d31),S(O)₂R^(b31) NR^(c31)S(O)₂R^(b31) S(O)₂NR^(c31)R^(d31) and oxo;

wherein each R^(Cy3B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy3B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy3B) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a31),SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy3B) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a31), SR^(a31),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31)NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo;

R³⁴ is selected from H and C₁₋₆ alkyl;

R³⁵ is selected from H, unsubstituted or substituted C₁₋₆ alkyl andCy^(3C), wherein the substituted C₁₋₆ alkyl forming R³⁵ is substitutedby 1, 2, 3, 4 or 5 substituents selected from the group consisting ofCy^(3C), halogen, CN, OR^(a31), SR^(a31), C(O)R^(b31),C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31), OC(O)NR^(c31)R^(d31),NR^(c31)R^(d31), NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(d31),NR^(c31)C(O)OR^(a31), C(═NR^(e31))NR^(c31)R^(d31),NR^(c31)C(═NR^(e31))NR^(c31)R^(d31), S(O)R^(b31), S(O)NR^(c31)R^(d31),S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31), S(O)₂NR^(c31)R^(d31) and oxo;provided that no more than one of the substituents of R³⁵ is Cy^(3C);

Cy^(3C) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(3C) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and

wherein the substituted C₆₋₁₀ aryl, substituted 5-10 memberedheteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(3C) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy3C), halogen, C₁₋₆haloalkyl, CN, OR^(a31), SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31),C(O)OR^(a31), OC(O)R^(b31), OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31),NR^(c31)C(O)R^(b31), NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), C(═NOR^(a31))NR^(c31)R^(d31),C(═NOC(O)R^(b31))NR^(c31)R^(d31), C(═NR^(e31))NR^(c31)C(O)OR^(a31),NR^(c31)C(═NR^(e31))NR^(c31)R^(d31), S(O)R^(b31), S(O)NR^(c31)R^(d31),S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31), S(O)₂NR^(c31)R^(d31) and oxo;

wherein each R^(Cy3C) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy3C) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy3C) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a31),SR^(a31), C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy3C) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a31), SR^(a3),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31)NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo;

R³⁶ is selected from H and C₁₋₆ alkyl;

R^(a3), R^(b31), R^(c31) and R^(d31) are each independently selectedfrom H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a3), R^(b31), R^(c31) and R^(d31) are each optionallysubstituted with 1, 2, 3, 4 or 5 substituents independently selectedfrom C₁₋₆ alkyl, halo, CN, OR¹², SR^(a32), C(O)R^(b32),C(O)NR^(c32)R^(d32), C(O)OR³², OC(O)R^(b32), OC(O)NR^(c32)R^(d32),NR^(c32)R^(d32), NR^(c32)C(O)R^(b32), NR^(c32)C(O)NR^(c32)R^(d32),NR^(c32)C(O)OR³², C(═NR^(e32))NR^(c32)R^(d32),NR^(c32)C(═NR^(e32))NR^(c32)R^(d32), S(O)R^(b32), S(O)NR^(c32)R^(d32),S(O)₂R^(b32), NR^(c32)S(O)₂R^(b32), S(O)₂NR^(c32)R^(d32) and oxo;

or R^(c31) and R^(d31) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each optionallysubstituted with 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, halo, CN, OR¹², SR³², C(O)R^(b32), C(O)NR^(c32)R^(d32), C(O)OR³²,OC(O)R^(b32), OC(O)NR^(c32)R^(d32), NR^(c32)R^(d32),NR^(c32)C(O)R^(b32), NR^(c32)C(O)NR^(c32)R^(d32), NR^(c32)C(O)OR^(a32),C(═NR^(e32))NR^(c32)R^(d32), NR^(c32)C(═NR^(e32))NR^(c32)R^(d32),S(O)R^(b32), S(O)NR^(c32)R^(d32), S(O)₂R^(b32), NR^(c32)S(O)₂R^(b32),S(O)₂NR^(c32)R^(d32) and oxo; R³², R^(b32), R^(c32) and R^(d32) are eachindependently selected from H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl,C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 membered heteroaryl, 4-7membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6 memberedheteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7 memberedheterocycloalkyl-C₁₋₃ alkyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl,C₂₋₆ alkenyl, C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 memberedheteroaryl, 4-7 membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6membered heteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7membered heterocycloalkyl-C₁₋₃ alkyl forming R³², R^(b32), R^(c32) andR^(d32) are each optionally substituted with 1, 2 or 3 substituentsindependently selected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxyand oxo;

or R^(c32) and R^(d32) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each of which isunsubstituted or substituted with 1, 2 or 3 substituents independentlyselected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo; and

R^(e31) and R^(e32) are each, independently, H, CN or NO₂.

In some embodiments, Cy^(3A) is unsubstituted or substituted aryl.

In some embodiments, Cy^(3A) is unsubstituted or substituted phenyl.

In some embodiments, Cy^(3A) is substituted phenyl.

In some embodiments, Cy^(3A) is substituted with at least one OR^(a31)or at least one C(═NR^(e31))NR^(c31)R^(d31),C(═NOR^(a31))NR^(c31)R^(d31), C(═NOC(O)R^(b31))NR^(c31)R^(d31), orC(═NR^(e31))NR^(c31)C(O)OR^(a31).

In some embodiments, Cy^(3A) is substituted with at least one OR^(a31)and by at least one additional substituent selected from the groupconsisting of C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(3A) is substituted with at least one OH and byat least one additional substituent selected from the group consistingof C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(3A) is substituted with at least oneC(═NR^(e31))NR^(c31)R^(d31), C(═NOR^(a31))NR^(c31)R^(d31),C(═NOC(O)R^(b31))NR^(c31)R^(d31), C(═NR^(e31))NR^(c31)C(O)OR^(a31),preferably in the 4-position.

In some embodiments, Cy^(3A) is substituted with at least oneC(═NR^(e31))NR^(c31)R^(d31), preferably in the 4-position.

In some embodiments, Cy^(3A) is substituted with at least one C(═NH)NH₂,preferably in the 4-position.

In some embodiments, Cy^(3A) is of any one of the following formulae:

In some embodiments, Cy^(3A) is of any one of the following formulae:

In some embodiments, in the formula defining Cy^(3A), R^(a31) is C₁₋₆alkyl, such as methyl; R^(b31) is C₁₋₆ alkyl, such as methyl, or R^(b31)is C₁₋₆ haloalkyl, such as trifluoromethyl and R^(c31) is alkyl such asmethyl.

In some embodiments, Cy^(3A) is unsubstituted or substituted heteroaryl.

In some embodiments, Cy^(3A) is unsubstituted or substitutedpyridin-3-yl, 1H-pyrrolo[2,3-b]pyridine-5-yl, or1H-benzo[d]imidazol-6-yl.

In some embodiments, Cy^(3A) is of any one of the following formulae:

In some embodiments, each R^(Cy3A) in the formula defining Cy^(3A) isindependently C₁₋₆ alkyl, such as methyl or ethyl, preferably methyl, orhalogen such as F, Cl or Br, preferably Cl, or amino.

In some embodiments, each R^(Cy3A) attached to nitrogen in the formuladefining Cy^(3A) is C₁₋₆ alkyl, such as methyl or ethyl.

In some embodiments, R³¹ is C₁₋₆ alkyl.

In some embodiments, R³¹ is methyl.

In some embodiments, R³¹ is H.

In some embodiments, R³² is H.

In some embodiments, R³² is C₁₋₆ alkyl.

In some embodiments, R³² is methyl.

In some embodiments, R³¹ and R³², together with the groups to which theyare attached, form a 4-6 membered heterocycloalkyl ring.

In some embodiments, the compound is according to any of the followingFormulae (III-1a) to (III-1h):

In some embodiments, R³³ is Cy^(3B).

In some embodiments, R³³ is. (C₁₋₆ alkylene)Cy^(3B), (C₂₋₆alkenylene)Cy^(3B), or (C₂₋₆ alkynylene)Cy^(3B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R³⁵ isunsubstituted.

In some embodiments, R³³ is (C₁₋₆ alkylene)Cy^(3B), (C₂₋₆alkenylene)Cy^(3B), or (C₂₋₆ alkynylene)Cy^(3B), wherein the C₁₋₆alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R³⁵ issubstituted by 1, 2, 3, 4 or 5 substituents each independently selectedfrom the group consisting of halogen, CN, OR^(a31), SR^(a31),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a1), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a1),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo.

In some embodiments, R³³ is Cy^(3B), (CR^(33A)R^(33B))_(n33)Cy^(3B).

In some embodiments, each R^(33A) is H.

In some embodiments, each R^(33B) is H.

In some embodiments, n33 is 0.

In some embodiments, n33 is 1.

In some embodiments, n33 is 2.

In some embodiments, n33 is 3.

In some embodiments, R³³ is CH₂Cy^(3B).

In some embodiments, R³³ is CH₂CH₂Cy^(3B).

In some embodiments, the compound is according to any of the followingFormulae (III-2) to (III-4):

In some embodiments, the compound is according to any of the followingFormulae (III-2a) to (III-2h):

In some embodiments, the compound is according to any of the followingFormulae (III-3a) to (III-3h):

In some embodiments, the compound is according to any of the followingFormulae (III-4a) to (III-4h):

In some embodiments, R³³ is CH₂CH₂CH₂Cy^(3B).

In some embodiments, Cy^(3B) is unsubstituted C₆₋₁₀ aryl.

In some embodiments, Cy^(3B) is unsubstituted phenyl.

In some embodiments, R³³ is CH₂CH₂Ph.

In some embodiments, Cy^(3B) is unsubstituted naphthyl, such as1-naphthyl or 2-naphthyl.

In some embodiments, R³³ is CH₂CH₂-1-naphthyl or CH₂CH₂-2-naphthyl.

In some embodiments, Cy^(3B) unsubstituted 5-10 membered heteroaryl.

In some embodiments, Cy^(3B) is unsubstituted pyridyl, such asunsubstituted 2-, 3-, or 4-pyridyl, unsubstituted quinolyl, such asunsubstituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl, unsubstitutedbenzo[b]thiophenyl such as unsubstituted 2-, 3-, 4-, 5-, 6-, or7-benzo[b]thiophenyl, or unsubstituted indolyl, such as unsubstitutedindol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or -7-yl.

In some embodiments, Cy^(3B) unsubstituted C₃₋₁₀ cycloalkyl.

In some embodiments, Cy^(3B) is unsubstituted cyclopentyl, cyclohexyl,or cycloheptyl.

In some embodiments, Cy^(3B) unsubstituted 4-10 memberedheterocycloalkyl.

In some embodiments, Cy^(3B) is substituted C₆₋₁₀ aryl.

In some embodiments, Cy^(3B) is substituted phenyl.

In some embodiments, Cy^(3B) is substituted naphthyl, such as 1-naphthylor 2-naphthyl.

In some embodiments, Cy^(3B) substituted 5-10 membered heteroaryl.

In some embodiments, Cy^(3B) is substituted pyridyl, such as substituted2-, 3-, or 4-pyridyl, substituted quinolyl, such as substituted 2-, 3-,4-, 5-, 6-, 7-, or 8-quinolyl, substituted benzo[b]thiophenyl such assubstituted 2-, 3-, 4-, 5-, 6-, or 7-benzo[b]thiophenyl, or substitutedindolyl, such as substituted indol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or-7-yl.

In some embodiments, Cy^(3B) substituted C₃₋₁₀ cycloalkyl.

In some embodiments, Cy^(3B) is substituted cyclopentyl, cyclohexyl, orcycloheptyl.

In some embodiments, Cy^(3B) substituted 4-10 membered heterocycloalkyl

In some embodiments, Cy^(3B) is substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy3B), halogen, andC₁₋₆ haloalkyl; wherein each R^(Cy3B) is independently selected fromC₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl and C₆₋₁₀ aryl or 5-10 memberedheteroaryl, wherein each C₆₋₁₀ aryl or 5-10 membered heteroaryl formingR^(Cy3B) is unsubstituted or substituted with 1, 2 or 3 substituentsindependently selected from halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, and haloalkyl.

In some embodiments, R³³ is selected from the following groups: phenyl;benzyl; 2-phenylethyl; 2,3-dihydro-1H-inden-2-yl;2-(2-methylphenyl)ethyl; 2-(3-methylphenyl)ethyl;2-(4-methylphenyl)ethyl; 2-(2,4-dimethylphenyl)ethyl;2-(2,5-dimethylphenyl)ethyl; 2-(3,5-dimethylphenyl)ethyl;2-(2-ethylphenyl)ethyl; 2-(3-ethylphenyl)ethyl; 2-(4-ethylphenyl)ethyl;2-(2,4-diethylphenyl)ethyl; 2-(2,5-dimethylphenyl)ethyl;2-(3,5-dimethylphenyl)ethyl; 2-(2-trifluoromethylphenyl)ethyl;2-(3-trifluoromethylphenyl)ethyl; 2-(4-trifluoromethylphenyl)ethyl;2-(2-fluorophenyl)ethyl; 2-(3-fluorophenyl)ethyl;2-(4-fluorophenyl)ethyl; 2-(2,4-difluorophenyl)ethyl;2-(2,5-difluorophenyl)ethyl; 2-(3,5-difluorophenyl)ethyl;2-(2-chlorophenyl)ethyl; 2-(3-chlorophenyl)ethyl;2-(4-chlorophenyl)ethyl; 2-(2,4-dichlorophenyl)ethyl;2-(2,5-dichlorophenyl)ethyl; 2-(3,5-dichlorophenyl)ethyl;2-(2-methoxyphenyl)ethyl; 2-(3-methoxyphenyl)ethyl;2-(4-methoxyphenyl)ethyl; 2-(2,4-dimethoxyphenyl)ethyl;2-(2,5-dimethoxyphenyl)ethyl; 2-(3,5-dimethoxyphenyl)ethyl;2-(cyclopentyl)ethyl; 2-(cyclohexyl)ethyl; 2-(cycloheptyl)ethyl;2-(2-(aminomethyl)phenyl)ethyl; 2-(3-(aminomethyl)phenyl)ethyl;2-(4-(aminomethyl)phenyl)ethyl; 2-(2-cyanophenyl)ethyl;2-(3-cyanophenyl)ethyl; and 2-(4-cyanophenyl)ethyl; and groups of thefollowing formulae:

In some embodiments, R³⁴ is hydrogen.

In some embodiments, R³⁴ is C₁₋₆ alkyl, such as methyl.

In some embodiments, R³⁵ is H.

In some embodiments, R³⁵ is Cy^(3C).

In some embodiments, R³⁵ is unsubstituted C₁₋₆ alkyl.

In some embodiments, R³⁵ is substituted C₁₋₆ alkyl.

In some embodiments, the substituted C₁₋₆ alkyl forming R³⁵ issubstituted by at least one substituent, wherein the substituents of R³⁵are independently selected from: 1, 2, or 3 substituents selected fromthe group consisting of Cy^(3C), halogen, CN, OR^(a31), SR^(a31),C(O)R^(b31), C(O)NR^(c31)R^(d31), C(O)OR^(a31), OC(O)R^(b31),OC(O)NR^(c31)R^(d31), NR^(c31)R^(d31), NR^(c31)C(O)R^(b31),NR^(c31)C(O)NR^(c31)R^(d31), NR^(c31)C(O)OR^(a31),C(═NR^(e31))NR^(c31)R^(d31), NR^(c31)C(═NR^(e31))NR^(c31)R^(d31),S(O)R^(b31), S(O)NR^(c31)R^(d31), S(O)₂R^(b31), NR^(c31)S(O)₂R^(b31),S(O)₂NR^(c31)R^(d31) and oxo.

In some embodiments, the substituted C₁₋₆ alkyl forming R³⁵ issubstituted by at least one substituent, wherein the substituentsinclude Cy^(3C).

In some embodiments, the substituted C₁₋₆ alkyl forming R³⁵ issubstituted by one substituent, wherein the substituent is Cy^(3C).

In some embodiments, R³⁵ is (CH₂)₁₋₅Cy^(3C).

In some embodiments, R³⁵ is CH₂Cy^(3C).

In some embodiments, Cy^(3C) is unsubstituted C₆₋₁₀ aryl.

In some embodiments, Cy^(3C) is unsubstituted phenyl or naphthyl, suchas 1-naphthyl or 2-naphthyl.

In some embodiments, Cy^(3C) is unsubstituted 5-10 membered heteroaryl.

In some embodiments, Cy^(3C) is unsubstituted pyridyl, such asunsubstituted 2-, 3-, or 4-pyridyl, unsubstituted quinolyl, such asunsubstituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl, unsubstitutedbenzo[b]thiophenyl such as unsubstituted 2-, 3-, 4-, 5-, 6-, or7-benzo[b]thiophenyl, or unsubstituted indolyl, such as unsubstitutedindol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or -7-yl.

In some embodiments, Cy^(3C) is unsubstituted C₃₋₁₀ cycloalkyl, such ascyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl.

In some embodiments, Cy^(3C) is unsubstituted 4-10 memberedheterocycloalkyl.

In some embodiments, Cy^(3C) is substituted C₆₋₁₀ aryl.

In some embodiments, Cy^(3C) is substituted phenyl, or substitutednaphthyl, such as substituted 1-naphthyl or 2-naphthyl.

In some embodiments, Cy^(3C) substituted 5-10 membered heteroaryl.

In some embodiments, Cy^(3C) is substituted pyridyl, such as substituted2-, 3-, or 4-pyridyl, substituted quinolyl, such as substituted 2-, 3-,4-, 5-, 6-, 7-, or 8-quinolyl, substituted benzo[b]thiophenyl such assubstituted 2-, 3-, 4-, 5-, 6-, or 7-benzo[b]thiophenyl, or substitutedindolyl, such as substituted indol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or-7-yl.

In some embodiments, Cy^(3C) is substituted C₃₋₁₀ cycloalkyl such assubstituted cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, orcycloheptyl.

In some embodiments, Cy^(3C) is substituted 4-10 memberedheterocycloalkyl.

In some embodiments, R³⁶ is H.

In some embodiments, R³⁶ is C₁₋₆ alkyl such as methyl.

In some embodiments, R^(a31), R^(b31), R^(c31), R^(d31), R^(a32),R^(b32), R^(c32) and R^(d32) are each independently selected from H andC₁₋₆ alkyl.

In some embodiments, each R^(e31) and each R^(e32) is H.

The compounds of Formula (III), and embodiments thereof, are useful asinhibitors of MASP-2 and for therapeutic use.

In some embodiments, the compounds of Formula (III), and embodimentsthereof, can be in the form of a salt such as a pharmaceuticallyacceptable salt.

The compounds of Formula (III), and embodiments thereof, are useful asinhibitors of MASP-2 and for therapeutic use. The compounds of Formula(III), and embodiments thereof, are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (III), or anembodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (III) or an embodiment thereofis provided in the form of a pharmaceutical composition comprising thecompound or a salt thereof, such as a pharmaceutically acceptable salt,and at least one pharmaceutically acceptable carrier or excipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (III) set forth in the Examples, including thecompounds listed in Table 31, e.g., the compounds with selectivity forMASP-2 over thrombin. In certain aspects, one or more of the variablesdefining the compounds of Formula (III) (such as Cy^(3A), R^(Cy3A)Cy^(3B), R^(Cy3B), Cy^(3C), R^(Cy3C), R³¹, R³², R³³, R^(33A), R^(33B),R³⁴, R³⁵, R³⁶, n33, R^(a31), R^(b31), R^(c31), R^(d31), R^(e31),R^(a32), R^(b32), R^(c32), R^(d32) and R^(e32)) is selected from thecorresponding substituents in the compounds of Formula (III) of theExamples, including the compounds listed in Table 31, preferably, thoseof the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

D. Compounds of Formula IV

In certain aspects, the present disclosure provides a compound ofFormula (IV).

or a salt thereof, for use in treating a MASP-2-associated disease ordisorder, wherein:

Cy^(4A) is unsubstituted or substituted C₆₋₁₀ aryl or unsubstituted orsubstituted 5-10 membered heteroaryl; wherein the ring atoms of the 5-10membered heteroaryl forming Cy^(4A) consist of carbon atoms and 1, 2, or3 heteroatoms selected from O, N and S; wherein the substituted C₆₋₁₀aryl or substituted 5-10 membered heteroaryl forming Cy^(4A) aresubstituted with 1, 2, 3, 4 or 5 substituents each independentlyselected from R^(Cy4A), halogen, C₁₋₆ haloalkyl, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(b41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo;

each R^(Cy4A) is independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl,C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl and4-10 membered heterocycloalkyl, wherein the ring atoms of the 5-10membered heteroaryl or 4-10-membered heterocycloalkyl forming R^(Cy4A)consist of carbon atoms and 1, 2, 3 or 4 heteroatoms selected from O, Nand S, wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl formingR^(Cy4A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, CN, OR^(a41),SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(a41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo, and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy4A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo;

R⁴¹ is H or C₁₋₆ alkyl, C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 memberedheteroaryl-C₁₋₆ alkyl, wherein the C₁₋₆ alkyl forming R⁴¹ isunsubstituted or substituted by 1, 2 or 3 substituents independentlyselected from halogen, CN, OR^(a41), SR^(a41), C(O)R¹¹,C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41), OC(O)NR^(c41)R^(d41),NR^(c41)R^(d41), NR^(c41)C(O)R^(b41), NR^(c41)C(O)NR^(c41)R^(d41),NR^(c41)C(O)OR^(a41), C(═NR^(e41))NR^(c41)R^(d41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(b41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo, andwherein the C₆₋₁₀ aryl-C₁₋₆ alkyl or 5-10 membered heteroaryl-C₁₋₆ alkylforming R⁴¹ is unsubstituted or substituted by 1, 2 or 3 substituentsindependently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆haloalkyl, CN, OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41),C(O)OR^(a41), OC(O)R^(b41), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41),NR^(c41)C(O)R^(b11), NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo;

R⁴² is H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, or Cy^(4B); whereineach of the C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl, forming R⁴² isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents selectedfrom the group consisting of Cy^(4B), halogen, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b1), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo; provided that no more than one of thesubstituents is Cy^(4B);

Cy^(4B) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor unsubstituted or substituted 4-10 membered heterocycloalkyl formingCy^(4B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; and wherein the substituted C₆₋₁₀ aryl, substituted 5-10membered heteroaryl substituted C₃₋₁₀ cycloalkyl, or 4-10 memberedheterocycloalkyl forming Cy^(4B) is substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy4B), halogen, C₁₋₆haloalkyl, CN, OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41),C(O)OR^(a41), OC(O)R^(b41), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41),NR^(c41)C(O)R^(b41), NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(b41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo;wherein each R^(Cy4B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10-membered heterocycloalkyl formingR^(Cy4B) consist of carbon atoms and 1, 2, or 3 heteroatoms selectedfrom O, N and S, and wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆alkynyl forming R^(Cy4B) is independently unsubstituted or substitutedwith 1, 2 or 3 substituents independently selected from halogen, CN,OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41),OC(O)R^(b1), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo; and each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingeach R^(Cy4B) is independently unsubstituted or substituted with 1, 2 or3 substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo;

or R⁴¹ and R⁴², together with the atoms to which they are attached andthe nitrogen atom linking the atoms to which R⁴¹ and R⁴² are attached,form a 4-7 membered heterocycloalkyl ring; which is optionally furthersubstituted by 1, 2, 3, 4 or 5 substituents each independently selectedfrom R^(Cy4B), halogen, C₁₋₆ haloalkyl, CN, OR^(a41), SR^(a41),C(O)R^(b1), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(b41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo;

R⁴³ is H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, or Cy^(4C); whereineach of the C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl forming R⁴³ isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents eachindependently selected from: 0, 1, 2, 3, 4 or 5 substituents selectedfrom the group consisting of Cy^(4C), halogen, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo, provided that no more than one substituentof the C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl forming R⁴³ is Cy^(4C);

Cy^(4C) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstituted orsubstituted 5-10 membered heteroaryl, unsubstituted or substituted C₃₋₁₀cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor unsubstituted or substituted 4-10 membered heterocycloalkyl formingCy^(4B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; and wherein the substituted C₆₋₁₀ aryl, substituted 5-10membered heteroaryl substituted C₃₋₁₀ cycloalkyl, or 4-memberedheterocycloalkyl forming Cy^(4C) is substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy4C), halogen, C₁₋₆haloalkyl, CN, OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41),C(O)OR^(a41), OC(O)R^(b41), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41),NR^(c41)C(O)R^(b41), NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(c41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo; eachR^(Cy4C) is independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl and 4-10membered heterocycloalkyl, wherein the ring atoms of the 5-10 memberedheteroaryl or 4-10-membered heterocycloalkyl forming R^(Cy4C) consist ofcarbon atoms and 1, 2, or 3 heteroatoms selected from O, N and S,wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl forming R^(Cy4C)is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, CN, OR^(a41),SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingeach R^(Cy4A) is independently unsubstituted or substituted with 1, 2 or3 substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R¹¹,S(O)₂NR^(c41)R^(d41) and oxo;

R^(a41), R^(b41), R^(c41) and R^(d41) are each independently selectedfrom H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, C₃₋₇cycloalkyl, 5-10 membered heteroaryl, 4-10 membered heterocycloalkyl,C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-10 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a41), R^(b41), R^(c41) and R^(d41) are each optionallysubstituted with 1, 2, 3, 4 or 5 substituents independently selectedfrom C₁₋₆ alkyl, halo, CN, OR^(a42), SR^(a42), C(O)R⁴²,C(O)NR^(c42)R^(d42), C(O)OR^(a42), OC(O)R^(b42), OC(O)NR^(c42)R^(d42),NR^(c42)R^(d42), NR^(c42)C(O)R^(b42), NR^(c42)C(O)NR^(c42)R^(d42),NR^(c42)C(O)OR^(a42), C(═NR^(e42))NR^(c42)R^(d42),NR^(c42)C(═NR^(e42))NR^(c42)R^(d42), S(O)R^(b42), S(O)NR^(c42)R^(d42),S(O)₂R^(b42), NR^(c42)S(O)₂R^(b42), S(O)₂NR^(c42)R^(d42) and oxo;

or R^(c41) and R^(d41) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each optionallysubstituted with 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, halo, CN, OR^(a42), SR^(a42), C(O)R^(b42), C(O)NR^(c42)R^(d42),C(O)OR^(a42), OC(O)R^(b42), OC(O)NR^(c42)R^(d42), NR^(c42)R^(d42),NR^(c42)C(O)R^(b42), NR^(c42)C(O)NR^(c42)R^(d42), NR^(c42)C(O)OR^(a42),C(═NR^(e42))NR^(c42)R^(d42), NR^(c42)C(═NR^(e42))NR^(c42)R^(d42),S(O)R^(b42), S(O)NR^(c42)R^(d42), S(O)₂R^(b42), NR^(c42)S(O)₂R^(b42),S(O)₂NR^(c42)R^(d42) and oxo;

R^(a42), R^(b42), R^(c42) and R^(d42) are each independently selectedfrom H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, phenyl,C₃₋₇ cycloalkyl, 5-6 membered heteroaryl, 4-7 membered heterocycloalkyl,phenyl-C₁₋₃ alkyl, 5-6 membered heteroaryl-C₁₋₃ alkyl, C₃₋₇cycloalkyl-C₁₋₃ alkyl and 4-7 membered heterocycloalkyl-C₁₋₃ alkyl,wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl,phenyl, C₃₋₇ cycloalkyl, 5-6 membered heteroaryl, 4-7 memberedheterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6 membered heteroaryl-C₁₋₃ alkyl,C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7 membered heterocycloalkyl-C₁₋₃ alkylforming R^(a42), R^(b42), R^(c42) and R^(d42) are each optionallysubstituted with 1, 2 or 3 substituents independently selected from OH,CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo;

or R^(c42) and R^(d42) attached to the same N atom, together with the Natom to which they are both attached, form a 4-, 5-, 6- or 7-memberedheterocycloalkyl group or 5-membered heteroaryl group, each of which isunsubstituted or substituted with 1, 2 or 3 substituents independentlyselected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆ alkyl)₂, halo, C₁₋₆alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxy and oxo; and

R^(e41) and R^(e42) are each, independently, H, CN or NO₂.

In some embodiments, Cy^(4A) is unsubstituted or substituted aryl.

In some embodiments, Cy^(4A) is unsubstituted or substituted phenyl.

In some embodiments, Cy^(4A) is substituted phenyl.

In some embodiments, Cy^(4A) is substituted with at least one OR^(a41)or at least one C(═NR^(e41))NR^(c41)R^(d41),C(═NOR^(a41))NR^(c41)R^(d41), C(═NOC(O)R^(b41))NR^(c41)R^(d41), orC(═NR^(e41))NR^(c41)C(O)OR^(a41).

In some embodiments, Cy^(4A) is substituted with at least one OR^(a41)and by at least one additional substituent selected from the groupconsisting of C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(4A) is substituted with at least one OH and byat least one additional substituent selected from the group consistingof C₁₋₆ alkyl, C₁₋₆ haloalkyl and halogen.

In some embodiments, Cy^(4A) is substituted with at least oneC(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),preferably in the 4-position.

In some embodiments, Cy^(4A) is substituted with at least oneC(═NR^(e41))NR^(c41)R^(d41), such as C(═NH)NH₂, preferably in the4-position.

In some embodiments, Cy^(4A) is of any one of the following formulae:

In some embodiments, in the formula defining Cy^(4A), R^(a41) is C₁₋₆alkyl, such as methyl, R^(b41) is C₁₋₆ alkyl, such as methyl, R^(b41) isC₁₋₆ haloalkyl, such as trifluoromethyl, and R^(c41) is alkyl such asmethyl.

In some embodiments, Cy^(4A) is unsubstituted or substituted heteroaryl.

In some embodiments, Cy^(4A) is unsubstituted or substitutedpyridin-3-yl, 1H-pyrrolo[2,3-b]pyridine-5-yl, or1H-benzo[d]imidazol-6-yl.

In some embodiments, Cy^(4A) is of any one of the following formulae:

In some embodiments, each R^(Cy4A) in the formula defining Cy^(4A) isindependently C₁₋₆ alkyl, such as methyl or ethyl, preferably methyl, orhalogen such as F, Cl or Br, preferably Cl.

In some embodiments, each R^(Cy4A) attached to nitrogen in the formuladefining Cy^(4A) is C₁₋₆ alkyl, such as methyl or ethyl.

In some embodiments, R⁴¹ is C₁₋₆ alkyl.

In some embodiments, R⁴¹ is H.

In some embodiments, R⁴¹ is methyl.

In some embodiments, R⁴² is H.

In some embodiments, R⁴² is unsubstituted C₁₋₆ alkyl, such as methyl.

In some embodiments, R⁴² is Cy^(4B).

In some embodiments, R⁴² is substituted C₁₋₆ alkyl, C₂₋₆ alkenyl, orC₂₋₆ alkynyl.

In some embodiments, R⁴² is substituted C₁₋₆ alkyl.

In some embodiments, R⁴² is substituted C₁₋₆ alkyl, wherein the C₁₋₆alkyl forming R⁴² is substituted by 1, 2, or 3 substituents selectedfrom the group consisting of Cy^(4B), halogen, CN, OR^(a41), SR^(a41),C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41), OC(O)R^(b41),OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41), NR^(c41)C(O)R^(b41),NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo; provided that no more than one of thesubstituents is Cy^(4B).

In some embodiments, the substituted C₁₋₆ alkyl forming R⁴² issubstituted by at least one substituent, wherein the substituentsinclude Cy^(4B).

In some embodiments, the substituted C₁₋₆ alkyl forming R³⁵ issubstituted by one substituent, wherein the substituent is Cy^(4B).

In some embodiments, R⁴² is (CH₂)₁₋₅Cy^(4B).

In some embodiments, R⁴² is CH₂Cy^(4B).

In some embodiments, Cy^(4B) is unsubstituted C₆₋₁₀ aryl such asunsubstituted phenyl or naphthyl, such as 1-naphthyl or 2-naphthyl,Cy^(4B) is unsubstituted 5-10 membered heteroaryl, such as unsubstitutedpyridyl, such as unsubstituted 2-, 3-, or 4-pyridyl, unsubstitutedquinolyl, such as unsubstituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl,unsubstituted benzo[b]thiophenyl such as unsubstituted 2-, 3-, 4-, 5-,6-, or 7-benzo[b]thiophenyl, or unsubstituted indolyl, such asunsubstituted indol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or -7-yl, Cy^(4B)is unsubstituted C₃₋₁₀ cycloalkyl, such as cyclopropyl, cyclobutyl,cyclopentyl, cyclohexyl, or cycloheptyl, or Cy^(4B) is unsubstituted4-10 membered heterocycloalkyl.

In some embodiments, Cy^(4B) is substituted C₆₋₁₀ aryl such assubstituted phenyl or naphthyl, such as 1-naphthyl or 2-naphthyl,Cy^(4B) is substituted 5-10 membered heteroaryl, such as substitutedpyridyl, such as substituted 2-, 3-, or 4-pyridyl, substituted quinolyl,such as substituted 2-, 3-, 4-, 5-, 6-, 7-, or 8-quinolyl, substitutedbenzo[b]thiophenyl such as substituted 2-, 3-, 4-, 5-, 6-, or7-benzo[b]thiophenyl, or substituted indolyl, such as substitutedindol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or -7-yl, Cy^(4B) is substitutedC₃₋₁₀ cycloalkyl, such as cyclopropyl, cyclobutyl, cyclopentyl,cyclohexyl, or cycloheptyl, or Cy^(4B) is substituted 4-10 memberedheterocycloalkyl.

In some embodiments, R⁴¹ and R⁴², together with the atoms to which theyare attached and the nitrogen atom linking the atoms to which R⁴¹ andR⁴² are attached, form a 4-7 membered heterocycloalkyl ring; which isoptionally further substituted by 1, 2, 3, 4 or 5 substituents eachindependently selected from R^(Cy4B), halogen, C₁₋₆ haloalkyl, CN,OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41), C(O)OR^(a41),OC(O)R^(b41), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41),NR^(c41)C(O)R^(b41), NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), C(═NOR^(a41))NR^(c41)R^(d41),C(═NOC(O)R^(b41))NR^(c41)R^(d41), C(═NR^(e41))NR^(c41)C(O)OR^(a41),NR^(c41)C(═NR^(e41))NR^(c41)R^(d41), S(O)R^(b41), S(O)NR^(c41)R^(d41),S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41), S(O)₂NR^(c41)R^(d41) and oxo.

In some embodiments, R⁴¹ and R⁴², together with the atoms to which theyare attached and the nitrogen atom linking the atoms to which R⁴¹ andR⁴² are attached, form a 5 or 6 membered heterocycloalkyl ring.

In some embodiments, the compound is according to any of the followingFormulae (IV-1), (IV-2), (IV-1a), (IV-1b), (IV-2a), or (IV-2b),

In some embodiments, R⁴³ is Cy^(4C).

In some embodiments, R⁴³ is unsubstituted C₁₋₆ alkyl.

In some embodiments, R⁴³ is substituted C₁₋₆ alkyl.

In some embodiments, the substituted C₁₋₆ alkyl forming R⁴³ issubstituted by at least one substituent independently selected from: 1,2, or 3 substituents selected from the group consisting of Cy^(4C),halogen, CN, OR^(a41), SR^(a41), C(O)R^(b41), C(O)NR^(c41)R^(d41),C(O)OR^(a41), OC(O)R^(b41), OC(O)NR^(c41)R^(d41), NR^(c41)R^(d41),NR^(c41)C(O)R^(b41), NR^(c41)C(O)NR^(c41)R^(d41), NR^(c41)C(O)OR^(a41),C(═NR^(e41))NR^(c41)R^(d41), NR^(c41)C(═NR^(e41))NR^(c41)R^(d41),S(O)R^(b41), S(O)NR^(c41)R^(d41), S(O)₂R^(b41), NR^(c41)S(O)₂R^(b41),S(O)₂NR^(c41)R^(d41) and oxo.

In some embodiments, the substituted C₁₋₆ alkyl forming R⁴³ issubstituted by at least one substituent, wherein the substituentsinclude Cy^(4C).

In some embodiments, the substituted C₁₋₆ alkyl forming R⁴³ issubstituted by one substituent, wherein the substituent is Cy^(4C).

In some embodiments, R⁴³ is (CH₂)₁₋₅Cy^(4C).

In some embodiments, R⁴³ is CH₂Cy^(4C).

In some embodiments, R⁴³ is CH₂CH₂Cy^(4C).

In some embodiments, R⁴³ is CF₂Cy^(4C) or CF₂CH₂Cy^(4C).

In some embodiments, Cy^(4C) is unsubstituted C₆₋₁₀ aryl, such asphenyl, 1-naphthyl or 2-naphthyl.

In some embodiments, Cy^(4C) is unsubstituted 5-10 membered heteroaryl,such as unsubstituted pyridyl, such as unsubstituted 2-, 3-, or4-pyridyl, unsubstituted quinolyl, such as unsubstituted 2-, 3-, 4-, 5-,6-, 7-, or 8-quinolyl, unsubstituted benzo[b]thiophenyl such asunsubstituted 2-, 3-, 4-, 5-, 6-, or 7-benzo[b]thiophenyl, orunsubstituted indolyl, such as unsubstituted indol-2-yl, -3-yl, -4-yl,-5-yl, -6-yl or -7-yl.

In some embodiments, Cy^(4C) is unsubstituted C₃₋₁₀ cycloalkyl, such ascyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, or cycloheptyl.

In some embodiments, Cy^(4C) is unsubstituted 4-10 memberedheterocycloalkyl.

In some embodiments, Cy^(4C) is substituted C₆₋₁₀ aryl, such assubstituted phenyl, substituted 1-naphthyl or substituted 2-naphthyl.

In some embodiments, Cy^(4C) is substituted 5-10 membered heteroaryl,such as substituted pyridyl, such as substituted 2-, 3-, or 4-pyridyl,substituted quinolyl, such as substituted 2-, 3-, 4-, 5-, 6-, 7-, or8-quinolyl, substituted benzo[b]thiophenyl such as substituted 2-, 3-,4-, 5-, 6-, or 7-benzo[b]thiophenyl, or substituted indolyl, such assubstituted indol-2-yl, -3-yl, -4-yl, -5-yl, -6-yl or -7-yl.

In some embodiments, Cy^(4C) is substituted C₃₋₁₀ cycloalkyl such assubstituted cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, orcycloheptyl.

In some embodiments, Cy^(4C) is substituted 4-10 memberedheterocycloalkyl.

In some embodiments, the compound is according to any of the followingFormulae (IV-3)-(IV-7), (IV-3a), (IV-3b), (IV-5a), (IV-5b), (IV-7a), or(IV-7b):

In some embodiments, R^(a41), R^(b41), R^(c41), R^(d41), R^(a42),R^(b42), R^(c42) and R^(d42) are each independently selected from H andC₁₋₆ alkyl.

In some embodiments, each R^(e41) and each R^(e42) is H.

In some embodiments, the compounds of Formula (IV), and embodimentsthereof, can be in the form of a salt such as a pharmaceuticallyacceptable salt.

The compounds of Formula (Iv), and embodiments thereof, are useful asinhibitors of MASP-2 and for therapeutic use. The compounds of Formula(IV), and embodiments thereof, are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (IV), or anembodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (IV) or an embodiment thereofis provided in the form of a pharmaceutical composition comprising thecompound or a salt thereof, such as a pharmaceutically acceptable salt,and at least one pharmaceutically acceptable carrier or excipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (IV) set forth in the Examples, including thecompounds listed in Table 31, (e.g., the compounds with selectivity forMASP-2 over thrombin). In certain aspects, one or more of the variablesdefining the compounds of Formula (IV) (such as Cy^(4A), R^(Cy4A)Cy^(4B), R^(Cy4B), Cy^(4C), R^(Cy4C), R⁴¹, R⁴², R⁴³, R^(a41), R^(b41),R^(c41), R^(d41), R^(e41), R^(a42), R^(b42), R^(c42), R^(d42) andR^(e42)) is selected from the corresponding substituents in thecompounds of Formula (IV) of the Examples, including the compoundslisted in Table 31, preferably, those of the compounds with selectivityfor MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

E. Compounds of Formula VA, VB, VIA, VIB, VIIA and VIIB 1. AdditionalChemical Definitions

The following definitions apply herein in the present section (II)(E)and the claims directed to the compounds of Formulae (VA), (VB), (VIA),(VIB), (VIIA) and (VIIB) disclosed herein.

The term “alkoxy” refers to a straight or branched chain saturated orunsaturated hydrocarbon containing at least one oxygen atom in an ethergroup (e.g., EtO-). The chain may contain an indicated number of carbonatoms. For example, “C₁-C₁₂ alkoxy” indicates that the group may havefrom 1 to 12 (inclusive) carbon atoms and at least one oxygen atom.Examples of C₁-C₁₂ alkoxy groups include, but are not limited to,methoxy, ethoxy, isopropoxy, butoxy, n-pentoxy, isopentoxy, neopentoxy,and hexoxy.

The term “alkyl” includes an aliphatic hydrocarbon chain that may bestraight chain or branched. The chain may contain an indicated number ofcarbon atoms: For example, C₁-C₁₂ indicates that the group may have from1 to 12 (inclusive) carbon atoms in it. If not otherwise indicated, analkyl group about 1 to about 20 carbon atoms. In one aspect, alkylgroups have 1 to about 12 carbon atoms in the chain. In another aspect,alkyl groups (“lower alkyl”) have 1 to about 6 carbon atoms in thechain. Examples may include, but are not limited to, methyl, ethyl,propyl, isopropyl (iPr), 1-butyl, 2-butyl, isobutyl (iBu), tert-butyl,pentyl, 2-methylbutyl, 1,1-dimethylpropyl, hexyl, heptyl, octyl, nonyl,decyl, dodecyl, cyclopentyl, or cyclohexyl. In one aspect, an alkylgroup can exclude methyl (e.g., 2 to 6 carbon atoms in the chain).

The term “aryl” as used herein includes cyclic aromatic carbon ringsystems containing from 6 to 18 carbons. Examples of an aryl groupinclude, but are not limited to, phenyl, naphthyl, anthracenyl,tetracenyl, biphenyl and phenanthrenyl.

The terms “arylalkyl” and “aralkyl,” which are used interchangeably,include an alkyl group as defined herein where at least one hydrogensubstituent has been replaced with an aryl group as defined herein.Examples include, but are not limited to, benzyl, 1-phenylethyl,4-methylbenzyl, and 1,1,-dimethyl-1-phenylmethyl.

The term “cycloalkyl” as used herein includes a cyclic hydrocarbon groupthat may contain an indicated number of carbon atoms: For example,C₃-C₁₂ indicates that the group may have from 3 to 12 (inclusive) carbonatoms in it. If not otherwise indicated, a cycloalkyl group includesabout 3 to about 20 carbon atoms. In one aspect, cycloalkyl groups have3 to about 12 carbon atoms in the group. In another aspect, cycloalkylgroups have 3 to about 7 carbon atoms in the group. Examples mayinclude, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl,cyclohexyl, 4,4-dimethylcyclohexyl, and cycloheptyl.

As used herein, “halo” or “halogen” includes fluoro, chloro, bromo, oriodo. In one aspect, “halo” includes fluoro or chloro (preferablychloro).

The term “heteroaryl” includes mono and bicyclic aromatic groups ofabout 4 to about 14 ring atoms (e.g., 4 to 10 or 5 to 10 atoms)containing at least one heteroatom. Heteroatom as used in the termheteroaryl refers to oxygen, sulfur and nitrogen. A nitrogen atom of aheteroaryl is optionally oxidized to the corresponding N-oxide. Examplesinclude, but are not limited to, pyrazinyl, furanyl, thienyl, pyridyl,pyrimidinyl, isoxazolyl, isothiazolyl, oxazolyl, thiazolyl, pyrazolyl,furazanyl, pyrrolyl, pyrazolyl, triazolyl, 1,2,4-thiadiazolyl,pyrazinyl, pyridazinyl, quinoxalinyl, phthalazinyl,imidazo[1,2-a]pyridine, imidazo[2,1-b]thiazolyl, benzofurazanyl,indolyl, azaindolyl, benzimidazolyl, benzothienyl, quinolinyl,imidazolyl, thienopyridyl, quinazolinyl, thienopyrimidyl,pyrrolopyridyl, imidazopyridyl, isoquinolinyl, benzoazaindolyl,1,2,4-triazinyl, and benzothiazolyl.

As used herein, “heterocyclyl” includes a non-aromatic saturatedmonocyclic or multicyclic ring system of about 4 to about 10 ring atoms(e.g., 5 to about 8 ring atoms, or 5 to about 6 ring atoms), in whichone or more of the atoms in the ring system is an element or elementsother than carbon, e.g., nitrogen, oxygen or sulfur. A heterocyclylgroup optionally comprises at least one sp²-hybridized atom (e.g., aring incorporating a carbonyl, endocyclic olefin, or exocyclic olefin).In some embodiments, a nitrogen or sulfur atom of the heterocyclyl isoptionally oxidized to the corresponding N-oxide, S-oxide orS,S-dioxide. Examples of monocyclic heterocyclyl rings include, but arenot limited to, piperidyl, pyrrolidinyl, piperazinyl, morpholinyl,thiomorpholinyl, thiazolidinyl, 1,3-dioxolanyl, 1,4-dioxanyl,tetrahydrofuranyl, tetrahydrothiophenyl, and tetrahydrothiopyranyl.

As used herein, the term “hydroxyalkyl” includes an alkyl group where atleast one hydrogen substituent has been replaced with an alcohol (—OH)group. In certain aspects, the hydroxyalkyl group has one alcohol group.In certain aspects, the hydroxyalkyl group has one or two alcoholgroups, each on a different carbon atom. In certain aspects, thehydroxyalkyl group has 1, 2, 3, 4, 5, or 6 alcohol groups. Examples mayinclude, but are not limited to, hydroxymethyl, 2-hydroxyethyl, and1-hydroxyethyl.

The term “hypertonic” refers to a formulation with an osmotic pressureabove that of human (i.e., greater than 350 mOsm/KglHhO).

When any two substituent groups or any two instances of the samesubstituent group are “independently selected” from a list ofalternatives, the groups may be the same or different. For example, ifR^(a) and R^(b) are independently selected from the group consisting ofalkyl, fluoro, amino, and hydroxyalkyl, then a molecule with two R^(a)groups and two R^(b) groups could have all groups be alkyl group (e.g.,four different alkyl groups). Alternatively, the first R^(a) could bealkyl, the second R^(a) could be fluoro, the first R^(b) could behydroxyalkyl, and the second R^(b) could be amino (or any othersubstituents taken from the group). Alternatively, both R^(a) and thefirst R^(b) could be fluoro, while the second R^(b) could be alkyl(i.e., some pairs of substituent groups may be the same, while otherpairs may be different).

As used herein, the term “salt” refers to acid or base salts of acompound, e.g., ZNA or another 2-(acylamino)imidazole. Illustrativeexamples of pharmaceutically acceptable salts are cationic salts such asalkali and alkaline earth metal (such as sodium, lithium, potassium,calcium, and magnesium) salts, ammonium (ammonium, trimethyl ammonium,diethylammonium, and tris-(hydroxymethyl)-methyl-ammonium) salts,mineral acid (hydrochloric acid, hydrobromic acid, phosphoric acid, andthe like) salts, organic carboxylic acid (acetic acid, propionic acid,glutamic acid, citric acid, and the like) salts, organic sulfonic acid(methanesulfonic acid) salts, and quaternary ammonium (methyl iodide,ethyl iodide, and the like) salts. Additional information on suitablepharmaceutically acceptable salts can be found in Remington's,Pharmaceutical Sciences (current edition), Mack Publishing Co., Easton,Pa., which is incorporated herein by reference.

The terms “a salt thereof,” “salt thereof,” or “salts thereof” can beapplied to any preceding member of an associated Markush group. Forexample, a group consisting of A, B, C, and salts thereof would includewithin its scope embodiments that were a salt of A, embodiments thatwere a salt of B, and embodiments that were a salt of C.

2. Compounds of Formula VA and VB

In certain aspects, the present disclosure provides a compound is of theFormula (VA) or (VB):

or a salt thereof; wherein:

A¹ is a member selected from the group consisting of —(C═NH)—,—(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, —[C═N[O(C═O)ZR^(b)]}—, a fused 5- or6-member heterocyclyl, and a fused 5- or 6-member heteroaryl;

when A¹ is —(C═NH)—, Y¹ is selected from the group consisting of —NH₂,—NH(C═O)R^(a), and —NH(C═O)ZR^(b);

when A¹ is —(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, or —{C═N[O(C═O)ZR^(b)]}—,Y¹ is —NH₂;

when A¹ is fused heterocyclyl or heteroaryl, Y¹ is —NH₂ or halo, and A¹is substituted with m additional R¹ groups;

each R^(a) and R^(b) is independently selected from the group consistingof C₁-C₆ alkyl, C₃-C₁₀ cycloalkyl, C₆-C₁₀ aryl, and C₇-C₁₂ arylalkyl;wherein R^(a) has m substituents selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively, R^(a)and R^(b) join to form a heterocyclyl ring with m substituents selectedfrom the group consisting of C₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, andhalo;

each Z is independently selected from the group consisting of O and S;

A² is a member selected from the group consisting of C₃-C₆ heteroaryl,C₆ aryl, and C₂-C₆ alkyl;

when A² is C₃-C₆ heteroaryl, Y² is selected from the group consisting of—NH₂, —CH₂NH₂, chloro, —(C═NH)NH₂, —(C═NH)NH(C═O)R^(a),—(C═NH)NH(C═O)ZR^(b), —(C═NOR^(a))NH₂, —[C═NO(C═O)R^(a)]NH₂, and—{C═N[O(C═O)ZR^(b)]}NH₂; and A² is substituted with m additional R¹groups;

when A² is C₆ aryl, Y² is selected from the group consisting ofaminomethyl, hydroxy, and halo, and A² is substituted with m additionalR¹ groups;

when A² is C₂-C₆ alkyl, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b);

each R¹ is a member independently selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆ alkylamino, and halo;

each m and n is an independently selected integer from 0 to 3;

L is —(O)_(p)—(C(R^(2a))(R^(2b)))_(q)—,

each R^(2a) or R^(2b) is a member independently selected from the groupconsisting of hydrogen and fluoro;

p is an integer from 0 to 1;

q is an integer from 1 to 2;

R³ is a member selected from the group consisting of hydrogen, C₁-C₆alkyl, C₁-C₆ fluoroalkyl, and carboxy(C₁-C₆ alkyl); or, alternatively,R³ and R⁴ join to form an azetidine, pyrrolidine, or piperidine ring;

R⁴ is a member selected from the group consisting of hydrogen and C₁-C₆alkyl; or, alternatively, R⁴ and R³ join to form an azetidine,pyrrolidine, or piperidine ring;

R⁵ is a member selected from the group consisting of C₃-C₇ cycloalkyl,C₄-C₈ cycloalkylalkyl, heteroaryl, and C₇-C₁₂ arylalkyl orheteroarylalkyl with from 0 to 3 R¹³ substituents; or, alternatively, R⁵and R⁶ join to form a heterocyclic ring with from 0 to 3 R¹³substituents;

R⁶ is a member selected from the group consisting of hydrogen, C₁-C₆alkyl, C₃-C₇ cycloalkyl, carboxy(C₁-C₆ alkyl), C₇-C₁₂ arylalkyl orheteroarylalkyl with from 0 to 3 R¹³ substituents, amino(C₁-C₈ alkyl);and amido(C₁-C₈ alkyl); or, alternatively, R⁶ and R⁵ join to form aheterocyclylic ring with from 0 to 3 R¹³ substituents; and

each R¹³ is a member independently selected from the group consisting ofC₁-C₆ alkyl, C₆-C₁₀ aryl, (C₆-C₁₀ aryl)C₁-C₆ alkyl, carboxy(C₁-C₆alkyloxy), heteroaryl, (C₆-C₁₀ heteroaryl)C₁-C₆ alkyl, heterocyclyl,hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉ alkoxyalkyl, amino,C₁-C₆ amido, C₁-C₆ alkylamino, and halo; or, alternatively, two R¹³groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀ heteroaryl, or C₅-C₇cycloalkyl ring.

In certain aspects, the present disclosure provides a compound is of theFormula (VA) or (VB):

or a salt thereof; wherein:

A¹ is a member selected from the group including —(C═NH)—,—(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, —[C═N[O(C═O)ZR^(b)]}—, a fused 5- or6-member heterocyclyl, and a fused 5- or 6-member heteroaryl;

when A¹ is —(C═NH)—, Y¹ is selected from the group including —NH₂,—NH(C═O)R^(a), and —NH(C═O)ZR^(b);

when A¹ is —(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, or —{C═N[O(C═O)ZR^(b)]}—,Y¹ is —NH₂;

when A¹ is fused heterocyclyl or heteroaryl, Y¹ is —NH₂ or halo, and A¹is substituted with m additional R¹ groups;

each R^(a) and R^(b) is independently selected from the group includingC₁-C₆ alkyl, C₃-C₁₀ cycloalkyl, C₆-C₁₀ aryl, and C₇-C₁₂ arylalkyl;wherein R^(a) has m substituents selected from the group including C₁-C₆alkyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉ alkoxyalkyl,amino, C₁-C₆ alkylamino, and halo; or, alternatively, R^(a) and R^(b)join to form an heterocyclyl ring with m substituents selected from thegroup including C₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, and halo;

each Z is independently selected from the group including O and S;

A² is a member selected from the group including C₃-C₆ heteroaryl, C₆aryl, and C₂-C₆ alkyl;

when A² is C₃-C₆ heteroaryl, Y² is selected from the group including—NH₂, —CH₂NH₂, chloro, —(C═NH)NH₂, —(C═NH)NH(C═O)R^(a),—(C═NH)NH(C═O)ZR^(b), —(C═NOR^(a))NH₂, —[C═NO(C═O)R^(a)]NH₂, and—{C═N[O(C═O)ZR^(b)]}NH₂; and A² is substituted with m additional R¹groups;

when A² is C₆ aryl, Y² is selected from the group including aminomethyl,hydroxy, and halo, and A² is substituted with m additional R¹ groups;

when A² is C₂-C₆ alkyl, Y² is selected from the group including—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b);

each R¹ is a member independently selected from the group includingC₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆ alkylamino, and halo;

each m and n is an independently selected integer from 0 to 3;

L is —(O)_(p)—(C(R^(2a))(R^(2b)))_(q)—,

each R^(2a) or R^(2b) is a member independently selected from the groupincluding hydrogen and fluoro;

p is an integer from 0 to 1;

q is an integer from 1 to 2;

R³ is a member selected from the group including hydrogen, C₁-C₆ alkyl,C₁-C₆ fluoroalkyl, and carboxy(C₁-C₆ alkyl); or, alternatively, R³ andR⁴ join to form an azetidine, pyrrolidine, or piperidine ring;

R⁴ is a member selected from the group including hydrogen and C₁-C₆alkyl; or, alternatively, R⁴ and R³ join to form an azetidine,pyrrolidine, or piperidine ring;

R⁵ is a member selected from the group including C₃-C₇ cycloalkyl, C₄-C₈cycloalkylalkyl, heteroaryl, and C₇-C₁₂ arylalkyl or heteroarylalkylwith from 0 to 3 R¹³ substituents; or, alternatively, R⁵ and R⁶ join toform a heterocyclic ring with from 0 to 3 R¹³ substituents;

R⁶ is a member selected from the group including hydrogen, C₁-C₆ alkyl,C₃-C₇ cycloalkyl, carboxy(C₁-C₆ alkyl), C₇-C₁₂ arylalkyl orheteroarylalkyl with from 0 to 3 R¹³ substituents, amino(C₁-C₈ alkyl);and amido(C₁-C₈ alkyl); or, alternatively, R⁶ and R⁵ join to form aheterocyclic ring with from 0 to 3 R¹³ substituents; and

each R¹³ is a member independently selected from the group includingC₁-C₆ alkyl, C₆-C₁₀ aryl, carboxy(C₁-C₆ alkyloxy), heteroaryl,heterocyclyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ amido, C₁-C₆ alkylamino, and halo; or,alternatively, two R¹³ groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀heteroaryl, or C₅-C₇ cycloalkyl ring,

with the proviso that the compound is not melagatran.

In certain aspects, the compound is of Formula VA.

In certain aspects, A¹ is —(C═NH)—. In certain aspects, A¹ is—NH(C═O)R^(a). In certain aspects, A¹ is —NH(C═O)ZR^(b). In certainaspects, Z is O, S, or N.

In certain aspects, A¹ is —(C═NH)—. In certain aspects, Y¹ is —NH₂. Incertain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, A¹ is —(C═NOR^(a))—. In certain aspects, Y¹ is —NH₂.In certain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, R^(a) or R^(b) is C₁-C₆ alkyl, such as methyl,ethyl, n-propyl, isopropyl, n-butyl, or t-butyl. In certain aspects,R^(a) or R^(b) is C₃-C₁₀ cycloalkyl, such as cyclohexyl, cyclopentyl, orcyclopropyl. In certain aspects, R^(a) or R^(b) is C₆-C₁₀ aryl, such asphenyl or substituted phenyl (e.g., 4-methoxyphenyl). In certainaspects, R^(a) or R^(b) is C₇-C₁₂ arylalkyl, such as benzyl or4-methoxybenzyl.

In certain aspects, A¹ is a fused heteroaryl. In certain aspects, A¹ isa quinolone. In certain aspects, A¹ is an isoquinoline. In certainaspects, A¹ is a benzimidazole. In certain aspects, Y¹ is —NH₂.

In certain aspects, Y¹ is-NH₂.

In certain aspects, the compound is of Formula VB.

In certain aspects, A² is C₆ aryl. In certain aspects, A² is C₃-C₆heteroaryl.

In certain aspects, A² is substituted with m additional R¹ groups, suchas halo, hydroxyl, C₂-C₆ alkyl, or C₁-C₄ methoxy,

In certain aspects, Y² is halo (e.g., chloro). In certain aspects, Y² is3-chloro. In certain aspects, Y² is aminomethyl (e.g., 4-aminomethyl).

In certain aspects, A² is C₂-C₆ alkyl.

In certain aspects, Y² is —NH(C═NH)NH₂.

In certain aspects, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b). Incertain aspects, Y² is —NH(C═NH)NH₂. In certain aspects, Y² is—NH(C═NH)NH(C═O)R^(a). In certain aspects, Y² is —NH(C═NH)NH(C═O)ZR^(b).

In certain aspects, the compound has an R³ stereochemistry of

In certain aspects, R³ is a member selected from the group includinghydrogen or methyl. In certain aspects, R³ is hydrogen. In certainaspects, R³ is methyl.

In certain aspects, R⁴ is a member selected from the group includinghydrogen or methyl. In certain aspects, R⁴ is hydrogen.

In certain aspects, R³ and R⁴ join to form an azetidine, pyrrolidine, orpiperidine ring. In certain aspects, R³ and R⁴ join to form apyrrolidine ring. In certain aspects, R³ and R⁴ join to form apiperidine ring.

In certain aspects, R⁵ is a member selected from the group including2,3-dihydro-1H-inden-2-yl, cyclohexyl, cyclohexylmethyl, phenyl, benzyl,phenethyl, and phenpropyl with from 0 to 3 R¹³ substituents.

In certain aspects, R⁵ is a member selected from the group includingphenethyl, 4-methylphenethyl, 4-chlorophenethyl, 4-fluorophenethyl, andphenpropyl. In certain aspects, R⁵ is a member selected from the groupincluding phenethyl, 4-methylphenethyl, 4-chlorophenethyl,4-fluorophenethyl, 3-methylphenethyl, 3-chlorophenethyl,3-fluorophenethyl, 2-methylphenethyl, 2-chlorophenethyl,2-fluorophenethyl, phenpropyl, 4-methylphenpropyl, 4-chlorophenpropyl,4-fluorophenpropyl, 3-methylphenpropyl, 3-chlorophenpropyl,3-fluorophenpropyl, 2-methylphenpropyl, 2-chlorophenpropyl, and2-fluorophenpropyl.

In certain aspects, R⁶ is a member selected from the group includingamino(C₁-C₈ alkyl). and C₇-C₁₂ arylalkyl with from 0 to 3 R¹³substituents.

In certain aspects, R⁶ is a member selected from the group includinghydrogen and carboxymethyl.

In certain aspects, R⁶ and R⁵ join to form a pyrrolidine,octahydro-1H-indole, 3-phenylpyrrolidine, piperidine,1,2,3,4-tetrahydroisoquinoline, 2,5-dihydro-1H-pyrrole, or1,2,3,6-tetrahydropyridine ring.

In certain aspects, R¹ is hydroxyl or C₁-C₆ alkoxy. In certain aspects,R¹ is hydroxyl (e.g., 2-hydroxy; 3-hydroxy). In certain aspects, R¹ ismethoxy (e.g., 2-methoxy).

In certain aspects, m is 0. In certain aspects, m is 1. In certainaspects, n is 0. In certain aspects, n is 1. In certain aspects, both mand n are 0.

In certain aspects, p is 0. In certain aspects, p is 1.

In certain aspects, q is 1. In certain aspects, p is 0 and q is 1.

In certain aspects, each R^(2a) or R^(2b) is hydrogen. In certainaspects, L is methylene. In certain aspects, L is ethylene.

In certain aspects, the compound of Formula (VA) is selected fromcompounds of Formulae (VC), (VD), (VE) and (VF):

and salts thereof; wherein:

R⁷ is a member selected from the group including hydrogen, hydroxyl, andC₁-C₆ alkyl;

R⁸ is a member selected from the group including hydrogen and C₁-C₆alkyl; and

each m and n is an independently selected integer from 0 to 2.

In certain aspects, the compound is of Formula (VC). In certain aspects,the compound is of Formula (VD). In certain aspects, the compound is ofFormula (VE). In certain aspects, the compound is of Formula (VF).

In certain aspects, R⁷ is hydrogen. In certain aspects, R⁸ is hydrogen.

The compounds of Formula (VA) and (VB), and embodiments thereof,including compounds of Formula (VC), (VD), (VE) and (VF), are useful asinhibitors of MASP-2 and for therapeutic use. The compounds of Formula(VA) and (VB), and embodiments thereof, are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (VA) or (VB),or an embodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (VA) or (VB) or an embodimentthereof is provided in the form of a pharmaceutical compositioncomprising the compound or a salt thereof, such as a pharmaceuticallyacceptable salt, and at least one pharmaceutically acceptable carrier orexcipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (VA) and (VB) in the Examples, including thecompounds listed in Table 31, e.g., the compounds with selectivity forMASP-2 over thrombin. In certain aspects, one or more of R¹, R^(a),R^(b), R^(2a), R^(2b), R³, R⁴, R⁵, R⁶, or R¹³ is selected from thecorresponding substituents in the compounds of (VA) and (VB) in theExamples, including the compounds listed in Table 31 preferably, thoseof the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

3. Compounds of Formula (VIA) and (VIB)

In certain aspects, the present disclosure provides a MASP-2 inhibitorycompound for therapeutic use, wherein the compound is of the Formula(VIA) or (VIB):

or a salt thereof; wherein:

A¹ is a member selected from the group consisting of —(C═NH)—,—(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, —[C═N[O(C═O)ZR^(b)]}—, a fused 5- or6-member heterocyclyl, and a fused 5- or 6-member heteroaryl;

when A¹ is —(C═NH)—, Y¹ is selected from the group consisting of —NH₂,—NH(C═O)R^(a), and —NH(C═O)ZR^(b);

when A¹ is —(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, or —{C═N[O(C═O)ZR^(b)]}—,Y¹ is —NH₂;

when A¹ is fused heterocyclyl or heteroaryl, Y¹ is —NH₂ or halo, and A¹is substituted with m additional R¹ groups;

each R^(a) and R^(b) is independently selected from the group consistingof C₁-C₆ alkyl, C₃-C₁₀ cycloalkyl, C₆-C₁₀ aryl, and C₇-C₁₂ arylalkyl;wherein R^(a) has m substituents selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively, R^(a)and R^(b) join to form an heterocyclyl ring with m substituents selectedfrom the group consisting of C₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, andhalo;

each Z is independently selected from the group consisting of O and S;

A² is a member selected from the group consisting of C₃-C₆ heteroaryland C₂-C₆ alkyl;

when A² is C₃-C₆ heteroaryl, Y² is selected from the group consisting of—NH₂, —CH₂NH₂, chloro, —(C═NH)NH₂, —(C═NH)NH(C═O)R^(a),—(C═NH)NH(C═O)ZR^(b), —(C═NOR^(a))NH₂, —[C═NO(C═O)R^(a)]NH₂, and—{C═N[O(C═O)ZR^(b)]}NH₂; and A² is substituted with m additional R¹groups;

when A² is C₂-C₆ alkyl, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b);

each R¹ is a member independently selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆ alkylamino, and halo;

each m and n is an independently selected integer from 0 to 3;

X and X² are each a member selected from the group consisting of NR⁸,CH, and CR¹⁰ (preferably, NR⁸); or, alternatively, the X and X² R¹⁰groups join to form a fused C₆ aryl, heteroaryl, or C₅-C₇ cycloalkylring with from 0 to 3 R¹³ substituents;

each R⁸ is a member independently selected from the group consisting ofhydrogen and C₁-C₆ alkyl;

each R¹⁰ is a member independently selected from the group consisting ofC₁-C₆ alkyl, heteroaryl or C₆-C₁₀ aryl with from 0 to 3 R¹³substituents, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively, twoR¹⁰ groups join to form a fused C₆ aryl, heteroaryl, or C₅-C₇ cycloalkylring with from 0 to 3 R¹³ substituents;

r is an integer from 0 to 4; and

each R¹³ is a member independently selected from the group consisting ofC₁-C₆ alkyl, C₆-C₁₀ aryl, carboxy(C₁-C₆ alkyloxy), heteroaryl,heterocyclyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ amido, C₁-C₆ alkylamino, and halo; or,alternatively, two R¹³ groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀heteroaryl, or C₅-C₇ cycloalkyl ring or a salt thereof.

In certain aspects, the compound is of Formula (VIA).

In certain aspects, the compound is of Formula (VIB).

In certain aspects, the compound is of Formula (VIC) or (VID):

or a salt thereof.

In certain aspects, each R⁷ is a member selected from the groupconsisting of hydrogen, hydroxyl, and C₁-C₆ alkyl; and m is an integerfrom 0 to 2.

In certain aspects, (i) the compound is of Formula (VIA) or a saltthereof, and m is 0; or (ii) the compound is (VIB) or a salt thereof,and r is 0.

In certain aspects, X is NR⁸.

In certain aspects, R⁸ is hydrogen.

In certain aspects, X² is CH or CR¹⁰.

In certain aspects, R¹⁰ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, C₆ aryl with from 0 to 3 R¹³substituents, C₁-C₆ alkoxy, and C₂-C₉ alkoxyalkyl.

In certain aspects, two R¹⁰ groups join to form a fused C₆ aryl ringwith from 0 to 3 R¹³ substituents.

In certain aspects, R⁷ is hydrogen.

In certain aspects, R³ is a member selected from the group consisting ofhydrogen or methyl. In certain aspects, R³ is methyl.

In certain aspects, Z is O.

In certain aspects, R¹¹ is (R¹⁴)(R¹⁴)N(CO)—.

In certain aspects, R¹¹ is (R¹⁴)(H)N(CO)—.

In certain aspects, R¹⁴ is C₁-C₆ alkyl, C₃-C₇ cycloalkyl, or C₄-C₈cycloalkylalkyl.

In certain aspects, R¹² is hydrogen or C₇-C₁₄ arylalkyl.

In certain aspects, R¹ is hydroxyl or C₁-C₆ alkoxy.

In certain aspects, each R^(2a) or R^(2b) is hydrogen.

In certain aspects, L is methylene.

In certain aspects, A¹ is —(C═NH)—. In certain aspects, Y¹ is —NH₂. Incertain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, A¹ is —(C═NOR^(a))—. In certain aspects, Y¹ is —NH₂.In certain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, A¹ is —(C═NH)—. In certain aspects, A¹ is—NH(C═O)R^(a). In certain aspects, A¹ is —NH(C═O)ZR^(b). In certainaspects, Z is O, S, or N.

In certain aspects, A¹ is a fused heteroaryl. In certain aspects, A¹ isa quinolone. In certain aspects, A¹ is an isoquinoline. In certainaspects, A¹ is a benzimidazole. In certain aspects, Y¹ is —NH₂.

In certain aspects, R^(a) or R^(b) is C₁-C₆ alkyl, such as methyl,ethyl, n-propyl, isopropyl, n-butyl, or t-butyl. In certain aspects,R^(a) or R^(b) is C₃-C₁₀ cycloalkyl, such as cyclohexyl, cyclopentyl, orcyclopropyl. In certain aspects, R^(a) or R^(b) is C₆-C₁₀ aryl, such asphenyl or substituted phenyl (e.g., 4-methoxyphenyl). In certainaspects, R^(a) or R^(b) is C₇-C₁₂ arylalkyl, such as benzyl or4-methoxybenzyl.

In certain aspects, R⁷ is hydrogen.

In certain aspects, the compound is of Formula (VIB).

In certain aspects, A² is C₃-C₆ heteroaryl.

In certain aspects, A² is substituted with m additional R¹ groups, suchas halo, C₂-C₆ alkyl, or C₁-C₄ methoxy,

In certain aspects, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b). Incertain aspects, Y² is —NH(C═NH)NH₂. In certain aspects, Y² is—NH(C═NH)NH(C═O)R^(a). In certain aspects, Y² is —NH(C═NH)NH(C═O)ZR^(b).

In certain aspects, Y² is halo (e.g., chloro, such as 3-chloro). Incertain aspects, Y² is aminomethyl (e.g., 4-aminomethyl).

In certain aspects, A² is C₂-C₆ alkyl.

In certain aspects, X is NR⁸ (e.g., NH or NMe). In certain aspects, X isCH. In certain aspects, X is CR¹⁰ (e.g., CMe).

In certain aspects, each Z is a member independently selected from thegroup consisting of O and NR⁸; and each R⁸ is a member independentlyselected from the group consisting of hydrogen and C₁-C₆ alkyl. Incertain aspects, one Z or each Z is NR^(b). In certain aspects, each R⁸is hydrogen.

In certain aspects, X² is NR⁸ (e.g., NH or NMe). In certain aspects, Bis CH. In certain aspects, X² is CR¹⁰ (e.g., CMe).

In certain aspects, the compound has an R³ stereochemistry of

In certain aspects, R³ is a member selected from the group consisting ofhydrogen or methyl. In certain aspects, R³ is hydrogen. In certainaspects, R³ is methyl.

In certain aspects, R¹ is hydroxyl or C₁-C₆ alkoxy. In certain aspects,R¹ is hydroxyl (e.g., 2-hydroxy; 3-hydroxy). In certain aspects, R¹ ismethoxy (e.g., 2-methoxy).

In certain aspects, m is 0. In certain aspects, m is 1. In certainaspects, n is 0. In certain aspects, n is 1. In certain aspects, both mand n are 0.

In certain aspects, p is 0. In certain aspects, p is 1.

In certain aspects, q is 1. In certain aspects, p is 0 and q is 1.

In certain aspects, each R^(2a) or R^(2b) is hydrogen. In certainaspects, L is methylene In certain aspects, L is ethylene.

In certain aspects, each R¹³ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, heteroaryl or C₆-C₁₀ aryl with from 0to 3 R¹³ substituents, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy,C₂-C₉ alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively,two R¹⁰ groups join to form a fused C₆ aryl, heteroaryl, or C₅-C₇cycloalkyl ring with from 0 to 3 R¹³ substituents. In certain aspects,an R¹⁰ is amino. In certain aspects, an R¹⁰ and an R¹ are amino.

In certain aspects, r is an integer from 0 to 5 (i.e., 0, 1, 2, 3, 4, or5). In certain aspects, r is an integer from 0 to 4 (i.e., 0, 1, 2, 3,and 4). In certain aspects, r is an integer from 0 to 3 (i.e., 0, 1, 2,or 3).

In certain aspects, each R¹³ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, C₆-C₁₀ aryl, carboxy(C₁-C₆ alkyloxy),heteroaryl, heterocyclyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy,C₂-C₉ alkoxyalkyl, amino, C₁-C₆ amido, C₁-C₆ alkylamino, and halo; or,alternatively, two R¹³ groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀heteroaryl, or C₅-C₇ cycloalkyl ring or a salt thereof. In certainaspects, R¹³ is phenyl. In certain aspects, R¹³ is substituted phenyl.

The compounds of Formula (VIA) and (VIB), and embodiments thereof,including compounds of Formula (VIC) and (VID), are useful as inhibitorsof MASP-2 and for therapeutic use. The compounds of Formula (VIA) and(VIB), and embodiments thereof, are useful in the treatment ofMASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (VIA) and(VIB), or an embodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (VIA) and (VIB) or anembodiment thereof is provided in the form of a pharmaceuticalcomposition comprising the compound or a salt thereof, such as apharmaceutically acceptable salt, and at least one pharmaceuticallyacceptable carrier or excipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (VIA) and (VIB) in the Examples, including thecompounds listed in Table 31, e.g., the compounds with selectivity forMASP-2 over thrombin. In certain aspects, one or more of R¹, R^(a),R^(b), R^(2a), R^(2b), R³, R⁴, R⁵, R⁶, or R¹³ is selected from thecorresponding substituents in the compounds of (VIA) and (VIB) in theExamples, including the compounds listed in Table 31 preferably, thoseof the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

4. Compounds of Formula VIIA and VIIB

In certain aspects, the present disclosure provides a MASP-2 inhibitorycompound for therapeutic use, wherein the compound is of the Formula(VIIA) or (VIIB):

or a salt thereof; wherein:

A¹ is a member selected from the group consisting of —(C═NH)—,—(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, —[C═N[O(C═O)ZR^(b)]}—, a fused 5- or6-member heterocyclyl, and a fused 5- or 6-member heteroaryl;

when A¹ is —(C═NH)—, Y¹ is selected from the group consisting of —NH₂,—NH(C═O)R^(a), and —NH(C═O)ZR^(b);

when A¹ is —(C═NOR^(a))—, —[C═NO(C═O)R^(a)]—, or —{C═N[O(C═O)ZR^(b)]—,Y¹ is —NH₂;

when A¹ is fused heterocyclyl or heteroaryl, Y¹ is —NH₂ or halo, and A¹is substituted with m additional R¹ groups;

each R^(a) and R^(b) is independently selected from the group consistingof C₁-C₆ alkyl, C₃-C₁₀ cycloalkyl, C₆-C₁₀ aryl, and C₇-C₁₂ arylalkyl;wherein R^(a) has m substituents selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively, R^(a)and R^(b) join to form an heterocyclyl ring with m substituents selectedfrom the group consisting of C₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, andhalo;

each Z is independently selected from the group consisting of O and S;

A² is a member selected from the group consisting of C₃-C₆ heteroaryland C₂-C₆ alkyl;

when A² is C₃-C₆ heteroaryl, Y² is selected from the group consisting of—NH₂, —CH₂NH₂, chloro, —(C═NH)NH₂, —(C═NH)NH(C═O)R^(a),—(C═NH)NH(C═O)ZR^(b), —(C═NOR^(a))NH₂, —[C═NO(C═O)R^(a)]NH₂, and—{C═N[O(C═O)ZR^(b)]}NH₂; and A² is substituted with m additional R¹groups;

when A² is C₂-C₆ alkyl, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b);

each R¹ is a member independently selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆ alkylamino, and halo;

each m and n is an independently selected integer from 0 to 3;

L is —(O)_(p)—(C(R^(2a))(R^(2b)))_(q)—,

each R^(2a) or R^(2b) is a member independently selected from the groupconsisting of hydrogen and fluoro;

p is an integer from 0 to 1;

q is an integer from 1 to 2;

R³ is a member selected from the group consisting of hydrogen, C₁-C₆alkyl, and carboxy(C₁-C₆ alkyl);

each R¹¹ is a member independently selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆ alkylamino, halo, and(R¹⁴)(R¹⁴)N(CO)—; or, alternatively, two R¹¹ groups join to form a fusedC₆ aryl, heteroaryl, or C₅-C₇ cycloalkyl ring with from 0 to 3 R¹³substituents;

r is an integer from 0 to 4; and

each Z is a member independently selected from the group consisting of Oand NR⁸;

each R⁸ is a member independently selected from the group consisting ofhydrogen and C₁-C₆ alkyl;

each R¹² is a member independently selected from the group consisting ofhydrogen, C₁-C₆ alkyl, and C₇-C₁₄ arylalkyl with from 0 to 3 R¹³substituents;

each R¹³ is a member independently selected from the group consisting ofC₁-C₆ alkyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively, twoR¹³ groups join to form a fused C₆ aryl, heteroaryl, or C₅-C₇ cycloalkylring; and

each R¹⁴ is a member independently selected from the group consisting ofhydrogen, C₁-C₆ alkyl, C₃-C₇ cycloalkyl, C₄-C₈ cycloalkylalkyl, C₇-C₁₄arylalkyl, and heteroaryl(C₁-C₆ alkyl); or, alternatively, two R¹³groups join to form a fused heterocyclyl ring.

In certain aspects, the compound is of Formula (VIIA).

In certain aspects, the compound is of Formula (VIIB).

In certain aspects, the compound is of Formula (VIIC):

in which each R⁷ is a member selected from the group consisting ofhydrogen, hydroxyl, and C₁-C₆ alkyl.

In certain aspects, R⁷ is hydrogen.

In certain aspects, X is NR⁸.

In certain aspects, R⁸ is hydrogen.

In certain aspects, X² is CH or CR¹⁰.

In certain aspects, R¹⁰ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, C₆ aryl with from 0 to 3 R¹³substituents, C₁-C₆ alkoxy, and C₂-C₉ alkoxyalkyl.

In certain aspects, two R¹⁰ groups join to form a fused C₆ aryl ringwith from 0 to 3 R13 substituents.

In certain aspects, R⁷ is hydrogen.

In certain aspects, R³ is a member selected from the group consisting ofhydrogen or methyl. In certain aspects, R³ is methyl.

In certain aspects, Z is O.

In certain aspects, R¹¹ is (R¹⁴)(R¹⁴)N(CO)—.

In certain aspects, R¹¹ is (R¹⁴)(H)N(CO)—.

In certain aspects, R¹⁴ is C₁-C₆ alkyl, C₃-C₇ cycloalkyl, or C₄-C₈cycloalkylalkyl.

In certain aspects, R¹² is hydrogen or C₇-C₁₄ arylalkyl.

In certain aspects, R¹ is hydroxyl or C₁-C₆ alkoxy.

In certain aspects, each R^(2a) or R^(2b) is hydrogen.

In certain aspects, L is methylene.

In certain aspects, A¹ is —(C═NH)—. In certain aspects, Y¹ is —NH₂. Incertain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, A¹ is —(C═NOR^(a))—. In certain aspects, Y¹ is —NH₂.In certain aspects, Y¹ is —NH(C═O)R^(a). In certain aspects, Y¹ is—NH(C═O)ZR^(b).

In certain aspects, A¹ is —(C═NH)—. In certain aspects, A¹ is—NH(C═O)R^(a). In certain aspects, A¹ is —NH(C═O)ZR^(b). In certainaspects, Z is O, S, or N.

In certain aspects, A¹ is a fused heteroaryl. In certain aspects, A¹ isa quinolone. In certain aspects, A¹ is an isoquinoline. In certainaspects, A¹ is a benzimidazole. In certain aspects, Y¹ is —NH₂.

In certain aspects, R^(a) or R^(b) is C₁-C₆ alkyl, such as methyl,ethyl, n-propyl, isopropyl, n-butyl, or t-butyl. In certain aspects,R^(a) or R^(b) is C₃-C₁₀ cycloalkyl, such as cyclohexyl, cyclopentyl, orcyclopropyl. In certain aspects, R^(a) or R^(b) is C₆-C₁₀ aryl, such asphenyl or substituted phenyl (e.g., 4-methoxyphenyl). In certainaspects, R^(a) or R^(b) is C₇-C₁₂ arylalkyl, such as benzyl or4-methoxybenzyl.

In certain aspects, R⁷ is hydrogen.

In certain aspects, the compound is of Formula (VIIB).

In certain aspects, A² is C₃-C₆ heteroaryl.

In certain aspects, A² is substituted with m additional R¹ groups, suchas halo, C₂-C₆ alkyl, or C₁-C₄ methoxy,

In certain aspects, Y² is selected from the group consisting of—NH(C═NH)NH₂, —NH(C═NH)NH(C═O)R^(a), and —NH(C═NH)NH(C═O)ZR^(b). Incertain aspects, Y² is —NH(C═NH)NH₂. In certain aspects, Y² is—NH(C═NH)NH(C═O)R^(a). In certain aspects, Y² is —NH(C═NH)NH(C═O)ZR^(b).

In certain aspects, Y² is halo (e.g., chloro, such as 3-chloro). Incertain aspects, Y² is aminomethyl (e.g., 4-aminomethyl).

In certain aspects, A² is C₂-C₆ alkyl.

In certain aspects, X is NR⁸ (e.g., NH or NMe). In certain aspects, X isCH. In certain aspects, X is CR¹⁰ (e.g., CMe).

In certain aspects, each Z is a member independently selected from thegroup consisting of O and NR⁸; and each R¹ is a member independentlyselected from the group consisting of hydrogen and C₁-C₆ alkyl. Incertain aspects, one Z or each Z is NR⁸. In certain aspects, each R⁸ ishydrogen.

In certain aspects, X² is NR⁸ (e.g., NH or NMe). In certain aspects, Bis CH. In certain aspects, X² is CR¹⁰ (e.g., CMe).

In certain aspects, the compound has an R³ stereochemistry of

In certain aspects, R³ is a member selected from the group consisting ofhydrogen or methyl. In certain aspects, R³ is hydrogen. In certainaspects, R³ is methyl.

In certain aspects, R¹ is hydroxyl or C₁-C₆ alkoxy. In certain aspects,R¹ is hydroxyl (e.g., 2-hydroxy; 3-hydroxy). In certain aspects, R¹ ismethoxy (e.g., 2-methoxy).

In certain aspects, m is 0. In certain aspects, m is 1. In certainaspects, n is 0. In certain aspects, n is 1. In certain aspects, both mand n are 0.

In certain aspects, p is 0. In certain aspects, p is 1.

In certain aspects, q is 1. In certain aspects, p is 0 and q is 1.

In certain aspects, each R^(2a) or R^(2b) is hydrogen. In certainaspects, L is methylene In certain aspects, L is ethylene.

In certain aspects, each R¹³ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, heteroaryl or C₆-C₁₀ aryl with from 0to 3 R¹³ substituents, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy,C₂-C₉ alkoxyalkyl, amino, C₁-C₆ alkylamino, and halo; or, alternatively,two R¹⁰ groups join to form a fused C₆ aryl, heteroaryl, or C₅-C₇cycloalkyl ring with from 0 to 3 R¹³ substituents. In certain aspects,an R¹⁰ is amino. In certain aspects, an R¹⁰ and an R¹ are amino.

In certain aspects, r is an integer from 0 to 5 (i.e., 0, 1, 2, 3, 4, or5). In certain aspects, r is an integer from 0 to 4 (i.e., 0, 1, 2, 3,and 4). In certain aspects, r is an integer from 0 to 3 (i.e., 0, 1, 2,or 3).

In certain aspects, each R¹³ is a member independently selected from thegroup consisting of C₁-C₆ alkyl, C₆-C₁₀ aryl, carboxy(C₁-C₆ alkyloxy),heteroaryl, heterocyclyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy,C₂-C₉ alkoxyalkyl, amino, C₁-C₆ amido, C₁-C₆alkylamino, and halo; or,alternatively, two R¹³ groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀heteroaryl, or C₅-C₇ cycloalkyl ring or a salt thereof. In certainaspects, R¹³ is phenyl. In certain aspects, R¹³ is substituted phenyl.

The compounds of Formula (VIIA) and (VIIB), and embodiments thereof,including compounds of Formula (VIIC) and (VIID), are useful asinhibitors of MASP-2 and for therapeutic use. The compounds of Formula(VIIA) and (VIIB), and embodiments thereof, are useful in the treatmentof MASP-2-associated diseases and disorders, and in the manufacture ofmedicaments for treating MASP-2-associated diseases and disorders. Thepresent disclosure also provides methods of treating a MASP-2-associateddisease and disorder comprising administering to a patient atherapeutically effective amount of a compound of Formula (VIIA) and(VIIB), or an embodiment thereof, optionally in the form of a salt.

In some embodiments the compound Formula (VIIA) and (VIIB) or anembodiment thereof is provided in the form of a pharmaceuticalcomposition comprising the compound or a salt thereof, such as apharmaceutically acceptable salt, and at least one pharmaceuticallyacceptable carrier or excipient.

In certain aspects, the compound is one or more selected from thecompounds of Formula (VIIA) and (VIIB) in the Examples, including thecompounds listed in Table 31, e.g., the compounds with selectivity forMASP-2 over thrombin. In certain aspects, one or more of R¹, R^(a),R^(b), R^(2a), R^(2b), R³, R⁴, R⁵, R⁶, or R¹³ is selected from thecorresponding substituents in the compounds of (VIIA) and (VIIB) in theExamples, including the compounds listed in Table 31 preferably, thoseof the compounds with selectivity for MASP-2 over thrombin.

In certain aspects, the invention sets forth a stereochemically pureenantiomer or diastereomer (e.g., an optically active compound with oneor more chiral centers). Unless specifically indicated otherwise, forany inventive compound with one or more stereocenters, the presentinvention is intended to include and to describe both the pure (+) and(−) enantiomers, any other diastereomers, mixtures that are enriched inan enantiomer or diastereomer (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%75%, 80%, 85, 90%, or 95% enantiomeric or diastereomeric excess), and aracemic mixture of enantiomers or diastereomers.

In certain aspects, the invention sets forth a pharmaceuticallyacceptable salt of the indicated chemical structure (e.g., ahydrohalide, such as a hydrochloride or dihydrochloride). Examples ofpharmaceutically acceptable salts are set forth in, e.g., Burge, S. M.et al., J. Pharm. Sci 1977, 66, 1-19. They include chlorides, bromides,iodides, formates, acetates, propionates, oxalates, malonates,succinates, fumarates, maleates, tartrates, citrates, benzoates,phthalates, sulfonates, arylsulfonates, alkylsulfonates, salts of fattyacids, and the like. Salts can be prepared by a variety of methods knownto the skilled artisan, including a precipitation with the conjugateacid or base (e.g., treatment with gaseous HCl or an HCl solution).

In certain aspects, the invention sets forth a prodrug. A prodrug is acompound that is converted to a biologically active form underphysiological conditions, often by hydrolysis, oxidation, or reduction(e.g., ester to acid form; carbamate to amino or hydroxy group;hydroxyamidine to amidine) Exemplary prodrugs are set forth in, e.g.,Tilley, J. W., “Prodrugs of Benzamide,” Prodrugs 2007, 191-222;Peterlin-Masic et al. Curr. Pharma. Design 2006, 12, 73-91. Prodrugs forthe amidine group include amidoximes, O-alkylamidoximes, acylamidines,carbamates, 1,2,4-oxadiazolin-4-ones, and the like.

In certain aspects, the compound is useful for selectively inhibitingMASP-2 over thrombin, the method comprising administering the compoundas described herein. In certain aspects, the selectivity ratio ofMASP-2:thrombin is at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1,5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1,18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

F. Compounds Defined by Reference to Binding Rules

In certain aspects, the present disclosure provides compounds havingMASP-2 inhibitory activity, especially for therapeutic use. The compoundwith MASP-2 inhibitory activity interacts with the MASP-2 serineprotease domain in an enzyme-inhibitor complex with a plurality ofintermolecular interactions. In certain aspects, the molecule isdescribed with complete specificity and description by the number andtype(s) of intermolecular interactions within a MASP-2 binding site,using an empirically derived rule set such as an interaction rule set.

In certain aspects, the compounds with MASP-2 inhibitory activityinteract with the MASP-2 serine protease domain as an enzyme-inhibitorcomplex. The compound having MASP-2 inhibitory activity has between 1and 100 intermolecular interactions between itself and MASP-2 such as 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75,76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100, or more intermolecular interactions withthe serine protease domain of MASP-2 (residues 445-686 of SEQ ID NO: 1).These intermolecular interactions types can be a hydrogen-bond, an ionicbond, an electrostatic bond, π-π interactions, a van der Waalsinteraction, binding of a water molecule or combinations thereof. Thenumbers within the various types of intermolecular interactions arecounted to reach a total.

In certain aspects, a plurality of the same type of intermolecularinteractions exists. For example, the enzyme-inhibitor complex may have1-40 hydrogen-bonds, 1-40 ionic bonds, 1-40 electrostatic bonds, 1-40π-π interactions, 1-40 van der Waals interactions, 1-40 binding of watermolecules and combinations of thereof, wherein each of the foregoing1-40 range means 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, or more interactions. In certain aspects, aplurality or multiple intermolecular interactions may exist with thesame amino acid within the binding site.

In certain instances, an inhibitory molecule is described by a rule set.The compound with MASP-2 inhibitory activity interacts with the MASP-2serine protease domain in an enzyme-inhibitor complex with a pluralityof intermolecular interactions or rules. In certain aspects, themolecule is described with complete structural and functionalspecificity and description by the number and type(s) of intermolecularinteractions. These rules have been empirically derived and discoveredusing crystallographic data with a number of enzyme-inhibitor complexco-crystals. In certain instances, the crystallographic data are from atleast 1, 10, 20, 30, 40, 50, up to 100 enzyme-inhibitor complexcrystals. For example, 30 co-crystals can be used, such as 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, or 30 or even more enzyme-inhibitor complexcrystals can be used to generate a set of rules. Using the co-crystalstructural information, it is possible to describe the binding site andinhibitory compounds within Angstrom detail and definition.

In certain instances, a plurality of amino acids within the MASP-2serine protease domain are involved in the intermolecular interactions.Amino acids within the MASP-2 serine protease domain (amino acidresidues 445-686 of SEQ ID NO:1) include, but are not limited to, ASP627, SER 628, SER 654, GLY 656, GLN 665, SER 657, PHE 529, TYR 607, TRP655, GLY 667, SER 633, ARG 630, CYS 629, HIS 483, PRO 606, PRO 608, SER611, VAL 653, MET 658, TYR 669, ASN 659, CYS 660, GLN 665.

In certain aspects, the number of amino acids within the serine proteasedomain that interact with a compound having MASP-2 inhibitory activityor that make up a rule set is about 1-50, or 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, or 50 amino acid residues within the MASP-2 serineprotease domain.

In certain instances, an inhibitor of the present disclosure is bound toMASP-2, rendering MASP-2 inactive. The amino acids of MASP-2 interactthrough intermolecular interactions with the inhibitor compound and thetypes of interactions are now described in more detail.

In certain aspects, the type of interactions include a hydrogen bond(H-bond). The enzyme-inhibitor complex may include 1-40 intermolecularH-bonds with one or more of the following 8 amino acids: ASP 627, SER628, SER 654, GLY 656, GLN 665, ARG 630, PRO 606 and SER 657. Theenzyme-inhibitor complex may include 1-40 intermolecular H-bonds withone or more of the following 6 amino acids: ASP 627, SER 628, SER 654,GLY 656, GLN 665 and SER 657. The 1-40 intermolecular H-bonds caninclude one or more atoms of the inhibitor with one or more atoms of ASP627, SER 628, SER 654, GLY 656, GLN 665, ARG 630, PRO 606 and SER 657.The 1-40 intermolecular H-bonds can include one or more atoms of theinhibitor with one or more atoms of ASP 627, SER 628, SER 654, GLY 656,GLN 665 and SER 657. Each amino acid can have more than one H-bondinteraction with an inhibitor. In certain instances, the same atom canbe hydrogen bonded to one or more partners. In other words, a singleatom of an inhibitory molecule can interact with 2 or more atoms on theprotein. In certain instances, there are 1-10H-bonds, or 2-8H-bonds, or1, 2, 3, 4, 5, 6, 7, 8, 9, or 10H-bonds per compounds.

In certain aspects, the type of interactions include an ionic and/or anelectrostatic interaction. The enzyme-inhibitor complex may include 1-10intermolecular ionic and/or electrostatic interactions with ASP 627 orARG 630. The enzyme-inhibitor complex may include 1-10 intermolecularionic and/or electrostatic interactions with ASP 627. ASP 627 can havemore than one ionic and or electrostatic interaction with an inhibitor.

In certain other aspects, the type of interaction is binding of a watermolecule with ASP 627, GLN 665, SER 657, ASN 659, SER 628, GLU 662, ARG630, VAL 668, TYR 602, TYR 607. The enzyme-inhibitor complex may include1-30 bound water molecules 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 tovarious amino acids, other water molecules, to the compounds orcombinations thereof.

In certain other instances, the type of interaction includes one or more(e.g., a plurality or 1-40) π-π interactions with one or more of thefollowing amino acids PHE 529, TYR 607, and/or TRP 655, 1, 2 or 3 aminoacids. Each of the foregoing amino acids can have more than one π-πinteraction.

In certain aspects, the type of interaction also includes one or moresuch as 1-40, van der Waals interactions with ALA 468, ALA 469, HIS 483,ASP 526, ALA 527, GLY 528, PHE 529, LEU 575, PRO 606, TYR 607, PRO 608,SER 611, ASP627, SER 628, CYS 629, ARG 630, GLY 631, ASP 632, SER 633,GLY634, GLY 635, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658,ASN 659, CYS 660, GLN 665, GLY 667, TYR 669 and combinations thereof,which interactions are specific MASP-2 amino acids within the serineprotease domain of MASP-2.

In certain aspects, the type of interaction also includes one or moresuch as 1-40, van der Waals interactions with HIS 483, PHE 529, PRO 606,TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS 629, ARG 630, SER 633,VAL 653, SER 654, TRP 655, GLY 656, SER 657, MET 658, ASN 659, CYS 660,GLN 665, GLY 667 and TYR 669 and combinations thereof, whichinteractions are specific MASP-2 amino acids within the serine proteasedomain of MASP-2.

In certain aspects, the MASP-2 inhibitory compound can be a compound asdescribed elsewhere herein, including the compounds of Formulae (I),(II), (III), (IV), (V), (VI) or (VII), or any of the embodimentsthereof.

In certain aspects, compounds having MASP-2 inhibitory activity comprisethe compounds of Formula (VIII):

In certain aspects, the compounds of the disclosure can have 5 segmentsidentified as M₁, M₂, M₃, M₄ and M₅. The segments or regions bind theactive binding site of MASP-2. In certain aspects, the various segmentsbind with affinity to the active site. The inhibitor recognition site orpocket includes the binding site for the inhibitor. Using thenomenclature of Schechter and Berger, P1-P1′ denotes the peptideresidues of the scissile bond of the substrate (inhibitor), whereasS1-S1′ denote the corresponding enzyme binding pocket for thesesegments. The inhibitor-MASP-2 interactions extends beyond the S1 siteand includes additional binding of the inhibitor to MASP-2. In oneaspect, M₁-M₅ may substantially bind to one or more binding pockets ofMASP-2. These binding pockets correspond to S1′, S1, S2, S3, and S4′.

In certain aspects, the disclosure provides compounds wherein M₁ is amember selected from the group consisting of:

wherein each R¹ is a member independently selected from the groupconsisting of C₁-C₆alkyl, hydroxyl, C₁-C₆ alkoxy, amino, C₁-C₆alkylamino, and halo (e.g., chloro);

each n is an independently selected integer from 0 to 4;

R⁷ is a member selected from the group consisting of hydrogen, hydroxyl,and C₁-C₆ alkyl; and

R⁸ is a member selected from the group consisting of hydrogen and C₁-C₆alkyl.

In certain aspects, M₅ has the formula:

R⁵ is a member selected from the group including C₃-C₇ cycloalkyl, C₄-C₈cycloalkylalkyl, heteroaryl, and C₇-C₁₂ arylalkyl or heteroarylalkylwith from 0 to 3 R¹³ substituents; or, alternatively, R⁵ and R⁶ join toform a heterocyclic ring with from 0 to 3 R¹³ substituents;

R⁶ is a member selected from the group consisting of hydrogen, C₁-C₆alkyl, C₃-C₇ cycloalkyl, carboxy(C₁-C₆ alkyl), C₇-C₁₂ arylalkyl orheteroarylalkyl with from 0 to 3 R¹³ substituents, amino(C₁-C₈ alkyl);and amido(C₁-C₈ alkyl); or, alternatively, R⁶ and R⁵ join to form aheterocyclic ring with from 0 to 3 R¹³ substituents; and

each R¹³ is a member independently selected from the group includingC₁-C₆ alkyl, C₆-C₁₀ aryl, carboxy(C₁-C₆ alkyloxy), heteroaryl,heterocyclyl, hydroxyl, hydroxyl(C₁-C₆ alkyl), C₁-C₆ alkoxy, C₂-C₉alkoxyalkyl, amino, C₁-C₆ amido, C₁-C₆ alkylamino, and halo; or,alternatively, two R¹³ groups join to form a fused C₆-C₁₀ aryl, C₆-C₁₀heteroaryl, or C₅-C₇ cycloalkyl ring.

In certain aspects, M₂₋₄ has the formula:

wherein R³ is a member selected from the group including hydrogen, C₁-C₆alkyl, C₁-C₆ fluoroalkyl, and carboxy(C₁-C₆ alkyl); or, alternatively,R³ and R⁴ join to form an azetidine, pyrrolidine, or piperidine ring;and

R⁴ is a member selected from the group including hydrogen and C₁-C₆alkyl; or, alternatively, R⁴ and R³ join to form an azetidine,pyrrolidine, or piperidine ring.

In certain aspects, the compounds having MASP-2 inhibitory activity ofFormula VIII have Formula VIIIA as follows:

Various interactions between a compound of Formula VIIIA and the MASP-2active site may exist as is shown in FIGS. 77A and 77B.

Segment M₁ of the compounds of Formula (VIIIA) can have an interactionwhich is an ionic type interaction between an ASP 627 carboxyl group anda positive (protonatable group) moiety in a compound of Formula (VIIIA).For example, as shown above, a nitrogen on the amidine can be aprotonatable moiety and ionically interact with ASP 627.

In certain other aspects, with respect to hydrogen bonding analysis,certain of the compounds of the disclosure interact throughintermolecular hydrogen bonding with one or more of the following aminoacids: ASP 627, SER 628, SER 654, GLY 656, GLN 665, ARG630, PRO606, SER633, CYS660 and SER 657 in MASP-2. In certain aspects, the compoundsinteract through intermolecular hydrogen bonding with one or more of thefollowing acids: ASP 627, SER 628, SER 654, GLY 656, GLN 665 and SER 657in MASP-2.

In certain aspects, the compound binds via H-bonds with 1, 2, 3, 4, 5 orall of the following residues: ASP 627, SER 628, SER 654, GLY 656, GLN665, ARG630, PRO606, SER 633, CYS660 and SER 657. In certain aspects,the compound binds via H-bonds with 1, 2, 3, 4, 5 or all of thefollowing residues: ASP 627, SER 628, SER 654, GLY 656, GLN 665 and SER657. There may be more than one H-bond per amino acid. In certainaspects, the number of hydrogen bonds between an inhibitory molecule andthe active site can be 1-40. In certain aspects, one amino acid (e.g.,GLY 656) may have more than 1 hydrogen bond. A compound of thedisclosure may have about 1 to about 10 hydrogen bonds, such as 2, 3, 4,5, 6, 7, 8, 9 or 10H-bonds.

In general, although crystal structural information does not directlyshow or detect hydrogen bonding, the LigPlot+ software used to describethe co-crystal structural information does include algorithms toevaluate the presence of (or “predict”) such H-bonding based on, e.g.,bond distances. Therefore, throughout the disclosure when a H-bond issaid to be present and described, it may be said to have been evaluatedby software to be present based on the crystallographic data.

In certain aspects, the compound binds via ionic or electrostaticinteractions or hydrogen bonding to ASP 627 or ARG630. In certainaspects, the compound does not bind via ionic interaction with ASP 627or ARG630. In certain aspects, the compound does bind via ionicinteraction with ASP 627 or ARG630. In certain aspects, the compoundbinds via ionic or electrostatic interactions or hydrogen bonding to ASP627. In certain aspects, the compound does not bind via ionicinteraction with ASP 627. In certain aspects, the compound does bind viaionic interaction with ASP 627.

As shown above, a hydrogen from a compound of Formula (VIIIA) in segmentM₁ hydrogen-bonds with SER 628 and another hydrogen from the compoundhydrogen-bonds with SER 657. In addition, hydrogens on SER 628 andanother on SER 657 hydrogen-bonds with nitrogens on the compound insegment M₁. In general, a hydrogen bond is a partially electrostaticattraction between a hydrogen (H) which is bound to a moreelectronegative atom such as nitrogen (N) or oxygen (O) and anotheradjacent atom bearing a lone pair of electrons.

As shown, in certain aspects, atoms in segment M₃ interact with SER 654.In certain aspects, an atom such as a nitrogen in segment M₃ hydrogenbonds with SER 654. In addition, in certain aspects, an atom such asnitrogen in M₃ is both a hydrogen bonding acceptor and donor with GLY656. In another aspect, an atom such as an oxygen in segment M₃interacts with a water molecule.

In certain aspects, an inhibitory compound interacts via a watermolecule. The water molecule may be bound to both the compound and anamino acid residue, only the compounds, only the amino acid or acombination thereof. The water molecule may bridge by binding M₁ and 1,2, 3, 4, 5, 6, or 7 MASP-2 residues ASP 627, GLN 665, SER 657, ASN 659,SER 628, GLU 662, ARG 630, VAL 668, TYR 602, TYR 607, VAL 668.

In certain aspects, the M₄ segment of a compound interacts through π-πstacking interactions with either TYR 607 and/or PHE 529 and in thevicinity of TRP 655. In certain other aspects, the compound interactsvia π-π interactions with 1, 2, 3 or all of the following residues: PHE529, TYR 607, and TRP 655. In certain aspects, π-π interactions of theedge-face or T-type interaction are present.

In yet certain other aspects, in order to minimize interactions withserine proteases other than MASP-2, such as thrombin, bulky aromaticgroups at segment M₄ of the compounds increase specificity for MASP-2over thrombin.

In yet certain other aspects, to minimize interactions with serineproteases other than MASP-2, such as thrombin, methylatedchloroazaindole M₁ segments of the compounds increase specificity forMASP-2 over thrombin.

In yet certain other aspects, to minimize interactions with serineproteases other than MASP-2, such as thrombin, large substituents suchas glutaminyl derivatives or small substituents such as fluorine on theglycine carbon or substitutions on the Nitrogen atom of the centerglycine of M₃ moieties increase specificity for MASP-2 over thrombin

In yet certain other aspects, to minimize interactions with serineprotease other than MASP-2, such as thrombin, planar aromatic groupssuch as 5-membered rings such as pyrazole connecting the M₃ region withthe M4 segments of the compounds increase specificity for MASP-2 overthrombin.

In certain aspects, a compound binds via 3H-bonds with 2 residues: SER654 and GLY 656. In certain aspects, there are two (2) H-bonds to GLY656. For example, in certain instances, only 3 hydrogen bonds existbetween the compound and the active site of MASP-2. In certain aspects,π-π stacking interaction (T-type or edge-face) can occur with either TYR607 or PHE 529 and in the vicinity of TRP 655. In other aspects, noionic bonds exist between the inhibitory compound and the active site ofMASP-2. In other aspects, ionic bonds exist between the inhibitorycompound and the active site of MASP-2.

In certain aspects, FIGS. 1-57 show certain of the amino acids of MASP-2having arcs with radiating lines showing interactions, such as van derWaals interactions, with atoms of inhibitors of the present disclosure.

In certain aspects, the compound interacts via van der Waals contacts to1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21 or all of the following residues: ALA 468, ALA 469, HIS 483, ASP 526,ALA527, GLY528, PHE 529, LEU 575, PRO 606, TYR 607, PRO608, SER 611,ASP627, SER 628, CYS 629, ARG 630, GLY 631, ASP 632, SER 633, GLY634,GLY 635, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658, ASN 659,CYS 660, GLN 665, GLY 667, TYR 669 and combinations thereof.

In certain aspects, the compound interacts via van der Waals contacts to1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21 or all of the following residues: GLY 667, SER 657, GLY 656, TRP 655,SER 654, SER 633, ARG 630, CYS 629, SER 628, ASP 627, PHE 529, HIS 483,PRO 606, TYR 607, PRO 608, SER 611, VAL 653, MET 658, TYR 669, ASN 659,CYS 660, GLN 665 and combinations thereof.

FIGS. 1-57 represent 2D ligand-MASP-2 interaction diagrams for specificcompounds of this disclosure. These figures are schematic depictions ofatoms from various compounds with those of MASP-2 amino acids ascomputed by LigPlot++ software settings for hydrogen-bond calculationparameters employing models derived from the correspondingcrystallographic MASP-2-compound co-structures. Atoms for amino acidsthat interact with compound atoms as well as compound atoms that havesufficient 2fo-fc electron density from crystallographic data aredepicted. MASP-2 amino acid residue numbering (MASP-2 AA #) is accordingto Uniprot accession code O00187, atom numbering for amino acids (AAatom) according to conventions established by the Protein Data Bank andcorrespond to those in Table A1 (Appendix). Hydrogen bonds and polarcontacts are depicted as broken lines with distances provided in unitsof Angstrom.

Turning now to FIG. 1 , an illustration of MASP-2 CCP2-SP amino acidinteractions with (1129) through hydrogen bonds.

As shown therein, six different hydrogen bonds are present between the(1129) compound atoms and the MASP-2 amino acid residue atoms. Inaddition, a total of four water molecules are shown in this area of theactive site to be included within the crystal structure, two of whichare shown to be participating in hydrogen bonding, either with one ormore atoms of the (1129) compound, or as a bridging water moleculebetween particular (1129) compound atoms and MASP-2 amino acid residueatoms. As shown therein, an amidine nitrogen N19 interacts with anoxygen OD1 of ASP 627 as a hydrogen bond donor. As used herein, when itis stated that the nitrogen acts as a “hydrogen bond donor” it meansthat a hydrogen (H) bound to a more electronegative atom such asnitrogen (N) is electrostatically attracted to an adjacent atom bearinga lone pair of electrons such as an oxygen. Nitrogen N19 also interactswith an oxygen of SER628 as a hydrogen bond donor. In addition, N20 ofthe amidine interacts with oxygen OE1 of GLN 665 and O of SER 657 as ahydrogen bond donor. The nitrogen N10 of the amide bond interacts byH-bonding as a donor with an oxygen of SER 654. Further, oxygen O07interacts by H-bonding with the nitrogen of GLY 656 as a hydrogen bondacceptor. Similarly, as above, when it is stated that an oxygen acts asa “hydrogen bond acceptor,” it means that a hydrogen (H) bound to a moreelectronegative atom such as nitrogen (N) is electrostatically attractedto or “accepted by” an adjacent atom such as oxygen bearing a lone pairof electrons. The oxygen O08 interacts with a water molecule near TRP655. The oxygen of O26 interacts with a water molecule, as does thesecondary amine N21, while the same water molecule further interactswith oxygen O3 of a nearby buffer molecule succinic acid (Sin1). Inaddition, the compound binds via ionic or electrostatic interaction toASP 627 (not shown).

FIG. 2 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1034) through hydrogen bonds. As shown therein, seven differenthydrogen bonds are present between the (1034) compound atoms and theMASP-2 amino acid residue atoms. The figure does not depict the presenceof any water molecules in the crystal structure. The amidine nitrogenN19 interacts with an oxygen of SER657 as a hydrogen bond donor. N19also interacts with oxygen OE1 of GLN665 as a hydrogen bond donor.Nitrogen N20 interacts with oxygen OE1 of GLN665, an oxygen of SER628,and the OD1 oxygen of ASP627 as a hydrogen bond donor. N10 nitrogeninteracts with oxygen of SER654 by H-bonding as a donor. Oxygen O07interacts with a nitrogen on GLY656 by H-bonding as an acceptor. Inaddition, the compound binds via ionic or electrostatic interaction toASP 627 (not shown).

FIG. 3 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1024) through hydrogen bonds. As shown therein, five different hydrogenbonds are present between atoms of the (1024) compound and MASP-2residue atoms. In addition, a total of six water molecules are shown inthe active site depicted to be included within the crystal structure,four of which are shown to be participating in hydrogen bonding, eitherwith one or more atoms of the (1024) compound, or as a bridging watermolecule between particular (1024) compound atoms and MASP-2 amino acidresidue atoms. As shown therein, the O2 oxygen interacts with a nitrogenof GLY 656 as a hydrogen bond acceptor. Nitrogen N1 interacts with twodifferent water molecules near TRP 655, one of which also interacts withoxygen O1. Nitrogen N2 interacts with another water molecule. The N3nitrogen interacts with an oxygen of SER 654 as a hydrogen bond donor.Amidine nitrogen N4 interacts with an oxygen of SER628 by H-bonding as adonor and OD2 oxygen of ASP 627 by H-bonding as a donor. The otheramidine nitrogen N5 interacts with an oxygen of SER 657 as a hydrogenbond donor and a nearby water molecule. The same water molecule that isinteracting with nitrogen N5 also interacts with oxygen OG of SER 657,an oxygen of GLN 665 via a hydrogen bond, and oxygen OD2 of ASP 627 as abridging water molecule. In addition, the compound binds via ionic orelectrostatic interaction ASP 627 (not shown).

FIG. 4 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1059) through hydrogen bonds. As shown therein, eight different H-bondsbetween the (1059) compound atoms and the MASP-2 residue atoms. Inaddition, a total of six water molecules are shown in the active sitedepicted to be included within the crystal structure, four of which areshown to be participating in hydrogen bonding, either with one or moreatoms of the (1059) compound, or as a bridging water molecule betweenparticular (1059) compound atoms and MASP-2 amino acid residue atoms. Asshown therein, the amine nitrogen of the benzimidazole moiety, N6, formshydrogen bonds as a donor with the OD2 oxygen of ASP 627, an oxygen ofGLN 665, and the oxygen OG of SER 657. Nitrogen N6 may also interactwith a water molecule. The same water molecule that is interacting withnitrogen N6 also interacts with oxygen OG of SER657 and an oxygen of ASN659 as a bridging water molecule. The hydrogen of the benzimidazole cantautomerize between N4 and N5. Although there is only one hydrogen,software shows that the benzimidazole nitrogen N4 interacts as a H-bonddonor with oxygen OD1 of ASP 627 and the other imidazole nitrogen N5interacts with an oxygen of SER 657 as a hydrogen bond donor. NitrogenN1 interacts with an oxygen of SER 654 as a hydrogen bond donor. OxygenO1 interacts with a nearby water molecule, which is a bridging watermolecule that further interacts with nitrogen NH1 of ARG 630 (anencircled cross) and nitrogen N3 of (1059). The N3 nitrogen interactswith another water molecule near TRP 655 as well as an oxygen of GLY 656as a hydrogen bond donor. Oxygen O2 interacts with the nitrogen of GLY656 as a hydrogen bond acceptor. The N2 nitrogen interacts with a watermolecule close to PHE 529. In addition, the compound binds via ionic orelectrostatic interaction to ASP 627 (not shown). The molecule labeledSo41 designates a sulfate ion.

FIG. 5 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1088) through hydrogen bonds. As shown therein, five different hydrogenbonds are present between atoms of the (1088) compound and atoms of theMASP-2 amino acid residues. In addition, a total of 17 water moleculesare shown to be included within the active site of the crystalstructure, seven of which are shown to be participating in hydrogenbonding with compound (1088), either with one or more atoms of the(1088), or as a bridging water molecule between particular (1088)compound atoms and MASP-2 amino acid residue atoms. As shown therein,nitrogen N31, the primary amine nitrogen of the isoquinoline moiety,interacts with the OG oxygen of SER 628 and the OD1 oxygen of ASP 627 asa hydrogen bond donor. The N31 nitrogen also interacts with a nearbywater molecule. The same water molecule that is interacting withnitrogen N31 also interacts with oxygen OG of SER628 and an oxygen ofVAL 668 as a bridging water molecule. The nitrogen of the isoquinolinering, N29, forms a hydrogen bond as a donor with oxygen OD2 of ASP 627and also forms a contact with a nearby water molecule. The same watermolecule that is interacting with nitrogen N29 also interacts withoxygen OD2 of ASP 627, both a nitrogen and oxygen OG of SER 657, and anoxygen atom of GLN665 as a bridging water molecule. Nitrogen N01interacts with an oxygen of SER654 as a hydrogen bond donor. NitrogenN05 interacts with a water molecule near GLY 656 and PHE 529, and oxygenO03 also interacts with two different water molecules that are locatedbetween PHE 529 and SER 654. Oxygen O07 interacts with the nitrogen ofGLY 656 as a hydrogen bond acceptor. The N18 nitrogen interacts with twodifferent water molecules, in which one of the water molecules alsointeracts with nitrogen NH1 of ARG 630 as a bridging water molecule. Inaddition, the compound binds via ionic or electrostatic interaction toASP 627 (not shown).

FIG. 6 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1036) through hydrogen bonds. As shown therein, six different hydrogenbonds are present between the (1036) compound atoms and the atoms of theMASP-2 residues. In addition, a total of four water molecules are shownto be included within the crystal structure, three of which are shown tobe participating in hydrogen bonding, either with one or more atoms ofthe (1036) compound, or as a bridging water molecule between particular(1036) compound atoms and MASP-2 amino acid residue atoms. As showntherein, an amidine nitrogen N26 interacts with an oxygen of SER 657 asa hydrogen bond donor. Nitrogen N26 also interacts with a watermolecule. The same water molecule that is interacting with nitrogen N26also interacts with oxygen OG of SER 657, an oxygen of ASN 659, anoxygen of GLN 665, and oxygen OD2 of ASP 627 as a bridging watermolecule. In addition, N27 of the amidine forms hydrogen bonds as adonor with oxygen OD2 of ASP 627 and an oxygen of SER 628. Nitrogen N17interacts with an oxygen of SER 654 as a hydrogen bond donor and oxygenO16 interacts with a water molecule positioned between ARG 630 and SER654. Oxygen O29 interacts with a nitrogen of GLY 656 as a hydrogen bondacceptor and the nitrogen of the pyrrolidine moiety, N03, interacts witha water molecule. In addition, the compound binds via ionic orelectrostatic interaction to ASP 627 (not shown).

FIG. 7 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1081) through hydrogen bonds. As shown therein, four different hydrogenbonds are present between atoms of the (1081) compound and atoms of theMASP-2 amino acid residues. In addition, a single water molecule isshown to be included within the crystal structure, which is shown to beparticipating in hydrogen bonding as a water molecule, bridging betweenone atom of the compound and multiple MASP-2 amino acid residue atoms.As shown therein, an amidine nitrogen N26 interacts with an oxygen ofSER 657 as a hydrogen donor. Nitrogen N26 also interacts with a watermolecule. The same water molecule that is interacting with nitrogen N26also interacts with oxygen OG of SER 657, an oxygen atom of GLN665, anoxygen atom of ASN 659, and oxygen OD2 of ASP 627 as a bridging watermolecule. The other amidine nitrogen, N27, interacts with an oxygen ofSER 628 as a hydrogen bond donor. Nitrogen N17 interacts with an oxygenof SER 654 as a hydrogen bond donor and nitrogen N03 interacts with anoxygen of GLY 656 as a hydrogen bond donor. In addition, the compoundbinds via ionic or electrostatic interaction ASP 627 (not shown).

FIG. 8 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1063) through hydrogen bonds. As shown therein, four different hydrogenbonds are present between the (1063) compound atoms and the MASP-2 aminoacid residue atoms. In addition, a total of two water molecules areshown to be included within the crystal structure, one of which is shownto be participating in hydrogen bonding with one atom of the (1063)compound. As shown therein, the amidine nitrogen N5 interacts with anoxygen of SER 657 as a hydrogen bond donor and the other amidinenitrogen N4 interacts with an oxygen of SER 628 as a hydrogen bonddonor. Nitrogen N3 interacts with an oxygen of SER 654 as a hydrogenbond donor, oxygen O2 interacts with a nearby water molecule, and oxygenO1 interacts with the nitrogen of GLY 656 as a hydrogen bond acceptor.In addition, the compound binds via ionic or electrostatic interactionASP 627 (not shown).

FIG. 9 is an illustration of MASP-2 CCP2-SP amino acid interactions with(1065) through hydrogen bonds. As shown therein, four different hydrogenbonds are present between the (1065) compound atoms and the MASP-2residue atoms. In addition, a total of seven water molecules are shownto be included within the crystal structure, five of which are shown tobe participating in hydrogen bonding, either with one or more atoms ofthe (1065) compound, or as a bridging water molecule between particular(1065) compound atoms and MASP-2 amino acid residue atoms. As showntherein, the amidine nitrogen N28 interacts with two different bridgingwater molecules, in which one of said water molecules further interactswith an oxygen atom of SER 657, while the second water moleculeinteracts with a nitrogen atom of SER 657, an oxygen OH of TYR 602, anoxygen atom of GLN 665, and oxygen OD2 of ASP 627. Nitrogen N28 alsoforms a hydrogen bond as a donor with oxygen OD2 of ASP 627. The otheramidine nitrogen N29 interacts as a hydrogen bond donor with the OD1oxygen of ASP627. Nitrogen N29 also interacts with a nearby watermolecule, bridging between N29, an oxygen atom of VAL 668, and oxygen OGof SER6 28. Nitrogen N14 interacts with an oxygen of SER 654 as ahydrogen bond donor and oxygen O13 interacts with a water molecule. Thesame water molecule that is interacting with O13 also interacts with anoxygen atom of ARG 630 as a bridging water molecule. Oxygen O09interacts with the nitrogen of GLY 656 as a hydrogen bond acceptor andthe nitrogen of the piperidine moiety, N06, interacts with a nearbywater molecule. In addition, the compound binds via ionic orelectrostatic interaction to ASP 627 (not shown).

FIG. 10 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1030) through hydrogen bonds. As shown therein, five differentH-bonds are present between the (1030) compound atoms and the MASP-2atoms. In addition, a total of three water molecules are shown to beincluded within the crystal structure, two of which are shown to beparticipating in hydrogen bonding with two different atoms of thecompound. As shown therein, the amidine nitrogen N4 interacts with anoxygen of SER 657 as a hydrogen bond donor and the other amidinenitrogen N5 interacts with oxygen OG of SER 628 as a hydrogen bonddonor. Nitrogen N3 interacts with an oxygen of SER 654 as a hydrogenbond donor, oxygen O1 interacts with a water molecule near PHE 529, andnitrogen N2 interacts with another nearby water molecule. Oxygen O2interacts with the nitrogen of GLY 656 as a hydrogen bond acceptor,while the nitrogen of the pyrrole moiety, N1, interacts with the oxygenof GLY 656 as a hydrogen bond donor. In addition, the compound binds viaionic or electrostatic interaction to ASP 627 (not shown).

FIG. 11 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1037) through hydrogen bonds. As shown therein, four differenthydrogen bonds are present between the (1037) molecule atoms and theMASP-2 amino acid residue atoms. The figure does not depict the presenceof any water molecules in the crystal structure. An amidine nitrogen N18interacts with an oxygen of SER 657 as a hydrogen bond donor. The otheramidine nitrogen N19 forms a hydrogen bond as a donor with oxygen OD2 ofASP 627. Nitrogen 09 interacts with an oxygen of SER 654 as a hydrogendonor and oxygen O04 interacts relatively weakly as a hydrogen acceptorwith the nitrogen of GLY 656. In addition, the compound binds via ionicor electrostatic interaction to ASP 627 (not shown).

FIG. 12 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1118) through hydrogen bonds. As shown therein, five differenthydrogen bonds are present between the atoms of (1118) and the atoms ofMASP-2 amino acids. In addition, a total of 17 water molecules are shownto be included within the crystal structure, five of which are shown tobe participating in hydrogen bonding, either with single atoms of the(1118) compound, or as a bridging water molecule between particular(1118) compound atoms and MASP-2 amino acid residue atoms. As showntherein, one of the amidine nitrogens, N4, interacts with an oxygen ofSER 657 as a hydrogen bond donor. Nitrogen N4 also interacts with abridging water molecule, bridging between N4, oxygen OG of SER 657, anoxygen atom of GLN 665, oxygen OD2 of ASP 627, and an oxygen atom of ASN659. The other amidine nitrogen N5 interacts with oxygen OG of SER 628as a hydrogen bond donor. Nitrogen N3 forms a hydrogen bond as a donorwith an oxygen of SER 654 and oxygen O2 interacts with two differentwater molecules close to PHE 529. Nitrogen N2 interacts with a nearbywater molecule as well. Oxygen O1 interacts with the nitrogen atom ofGLY 656 as a hydrogen bond acceptor, while nitrogen N1 interacts withthe oxygen atom of GLY 656 as a hydrogen bond donor. Nitrogen N1 alsointeracts with a water molecule. In addition, the compound binds viaionic or electrostatic interaction to ASP 627 (not shown).

FIG. 13 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1090) through hydrogen bonds. As shown therein, five differenthydrogen bonds are present between the (1090) atoms and the MASP-2residue atoms. In addition, a total of two water molecules are shown tobe included within the crystal structure, both of which are shown to beparticipating in hydrogen bonding, either with a single atom of (1090)or as a water molecule, bridging between one atom of the (1090) compoundand multiple MASP-2 amino acid residue atoms. As shown therein, nitrogenN5, the amine nitrogen of the isoquinoline moiety, interacts with anearby water molecule. This water molecule also interacts with oxygen OGof SER 657 and an oxygen atom of GLN 665 as a bridging water molecule.Nitrogen N5 also interacts with an oxygen of SER 657 as a hydrogen bonddonor. The nitrogen of the isoquinoline ring, N4, interacts with oxygenOD2 of ASP 627 as a hydrogen bond donor. Nitrogen N2 interacts with anoxygen of SER 654 as a hydrogen bond donor and oxygen O1 interacts witha nearby water molecule positioned next to SER 654. Oxygen O2 interactswith the nitrogen atom of GLY 656 as a hydrogen bond acceptor and thenitrogen of the pyrrolidine moiety, N1, interacts with the oxygen atomof GLY 656 as a hydrogen bond donor.

FIG. 14 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1007) through hydrogen bonds. As shown therein, four differenthydrogen bonds exist between the (1007) compound atoms and the MASP-2amino acid residue atoms. In addition, a total of three water moleculesare shown to be included within the crystal structure, all of which areshown to be participating in hydrogen bonding, either with single atomsof the (1007) compound, or as a bridging water molecule betweenparticular (1007) compound atoms and MASP-2 amino acid residue atoms. Asshown therein, nitrogen N5, the amine nitrogen of the pyridine moiety,interacts with OD2 oxygen of ASP 627 and an oxygen of SER 657 as ahydrogen bond donor. The nitrogen of the pyridine ring, N1, interactswith an oxygen of SER 628 as a hydrogen bond donor. Nitrogen N1 alsointeracts with a water molecule. This water molecule bridges between N1of (1007), oxygen OD1 of ASP 627, oxygen OG of SER 628, as well as theother oxygen atom of SER628. Nitrogen atom N2 interacts with an oxygenof SER 654 as a hydrogen bond donor and nitrogen atom N4 interacts withtwo different water molecules, one of which is a bridging water moleculewhich interacts with NH1 of ARG 630. In addition, the compound binds viaionic or electrostatic interaction to ASP 627 (not shown).

FIG. 15 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1021) through hydrogen bonds. As shown therein, two differenthydrogen bonds are present between (1021) and MASP-2 amino acid atoms.In addition, a single water molecule is shown to be included within thecrystal structure, which is shown to be participating in hydrogenbonding as a water molecule, bridging between one atom of the (1021)compound and an atom of a MASP-2 amino acid residue. As shown therein,the amide nitrogen N1 interacts with an oxygen of SER 654 as a hydrogenbond donor. The amino nitrogen N3 interacts with a bridging watermolecule which also interacts with the phenolic OH-group of TYR 607.Oxygen O1 interacts with the nitrogen of GLY 656 as a hydrogen bondacceptor. In addition, the compound does not bind via ionic orelectrostatic interaction to ASP 627.

FIG. 16 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1097) through hydrogen bonds. As shown therein, six differentH-bonds are present between the (1097) compound atoms and the MASP-2residue atoms. In addition, a total of five water molecules are shown tobe included within the crystal structure, four of which are shown to beparticipating in hydrogen bonding, either with one or more atoms of the(1097) compound, or as a bridging water molecule between particular(1097) compound atoms and MASP-2 amino acid residue atoms. As showntherein, an amidine nitrogen, N6, interacts with an oxygen of SER 657 asa hydrogen bond donor. Nitrogen N6 also interacts with a bridging watermolecule that is positioned between and interacting with oxygen OG ofSER 657 and an oxygen atom of GLN665. In addition, N5 of the amidineinteracts with oxygen OD2 of ASP 627 and an oxygen atom of SER 628 as ahydrogen bond donor. Nitrogen N4 forms a hydrogen bond as a donor withan oxygen of SER 654 and nitrogen N3 interacts with a nearby watermolecule. Oxygen O1 (in the backbone) and nitrogen N1 in the piperidinylring of the fused tetrahydro-pyrido-indole system interact with the samebridging water molecule positioned between HIS 483 and GLY 656. The N1nitrogen also interacts with the oxygen of GLY 656 as a hydrogen bonddonor and the 02 oxygen interacts with the nitrogen atom of the GLY 656as a hydrogen bond acceptor. Nitrogen N2 in the indole ring of the fusedtetrahydro-pyrido-indole system interacts with a water molecule shownbetween TRP 655 and SER 657. In addition, the compound binds via ionicor electrostatic interaction to ASP 627 (not shown).

FIG. 17 is an illustration of MASP-2 CCP2-SP amino acid interactionswith (1089) through hydrogen bonds. As shown therein, five differenthydrogen bonds are present between atoms of the (1089) compound and theatoms of the MASP-2 amino acid residues. In addition, a total of ninewater molecules are shown to be included within the crystal structure,three of which are shown to be participating in hydrogen bonding, eitherwith single atoms of the (1089) compound, or as a bridging watermolecule between particular (1089) compound atoms and MASP-2 amino acidresidue atoms. As shown therein, nitrogen N5, the primary amine nitrogenof the isoquinoline moiety, interacts with an oxygen atom of SER 657 asa hydrogen bond donor. The N5 nitrogen also interacts with a bridgingwater molecule that is positioned between and interacting with oxygen OGof SER 657, an oxygen atom of GLN 665, and oxygen OD2 of ASP627. Thenitrogen of the isoquinoline ring, N4, interacts with oxygen OD2 of ASP627 as a hydrogen bond donor. Nitrogen N3 forms a hydrogen bond as adonor with an oxygen of SER654 and oxygen O1 interacts with a nearbywater molecule. The oxygen O2 forms a hydrogen bond as an acceptor withthe nitrogen atom of GLY 656, while the pyrrolidinyl nitrogen N1interacts with the oxygen atom of GLY 656 as a hydrogen bond donor.Nitrogen N1 also interacts with a nearby water molecule. In addition,the compound binds via ionic or electrostatic interaction to ASP 627(not shown).

FIG. 18 is an illustration of MASP-2 CCP2-SP amino acid interactionswith melagatran via hydrogen bonds. As shown therein, two differentH-bonds exist between the atoms of melagatran and the atoms of theMASP-2 residues. The figure does not depict the presence of any watermolecules in the crystal structure. One of the amidine nitrogens, N25,interacts with an oxygen of SER 657 as a hydrogen bond donor and theother amidine nitrogen N24 interacts with an oxygen of SER 628 as ahydrogen bond donor. In addition, the compound binds via ionic orelectrostatic interactions or hydrogen bonding to ASP 627 (not shown).

FIG. 19 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound 14 via hydrogen bonds. The compound binds covalently toSER 633 with opening of the oxazin-4-one ring. The carbonyl oxygen atomO2 of the resulting ester linkage forms a hydrogen bond with nitrogenNE2 of HIS 483 as a hydrogen bond acceptor. Furthermore, the samecarbonyl oxygen atom also forms a hydrogen bond with water molecule 66as a hydrogen bond acceptor.

FIG. 20 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (54) via hydrogen bonds. As shown therein, two differentH-bonds exist between the atoms of compound (54) and the atoms of theMASP-2 residues. The carbonyl oxygen atom O09, interacts with an oxygenof SER 628 as a hydrogen bond acceptor and the amino nitrogen atom N15interacts with a carbonyl oxygen of SER 657 as a hydrogen bond donor. Inaddition, one water molecule is included within the crystal structure,which is shown to be participating as a bridging water molecule betweenthe carbonyl oxygen atom O09 of compound (54) and MASP-2 amino acidresidue atoms of SER 628, TRP 655 and VAL 668.

FIG. 21 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1042) through hydrogen bonds. As shown therein, fourdifferent hydrogen bonds are present between the compound (1042) atomsand the MASP-2 amino acid residue atoms. As shown therein, an amidinenitrogen N21 interacts with a carbonyl oxygen O of SER 657 as a hydrogenbond donor. The other amidine nitrogen N22 interacts with a carbonyloxygen O of SER 628 as a hydrogen bond donor and with a carboxylategroup oxygen OD1 of ASP 627 as a hydrogen bond donor. The amino groupnitrogen N03 interacts with a carbonyl oxygen of GLY 656 as a hydrogenbond donor.

FIG. 22 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (2018) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (2018)compound atoms and the MASP-2 amino acid residue atoms. As showntherein, one of the amidine nitrogens, N4, interacts with a carbonyloxygen O of SER 657 as a hydrogen bond donor and with a carbonyl oxygenOE1 of SER 657 as a hydrogen bond donor. The other amidine nitrogen N5interacts with an oxygen of SER 628 as a hydrogen bond donor. The amidenitrogen N3 interacts with the carbonyl oxygen O of SER 654 as ahydrogen bond donor, and with the hydroxyl oxygen OG of SER 633 as ahydrogen bond acceptor. The carbonyl oxygen O2 interacts with thenitrogen N of GLY 656 as a hydrogen bond acceptor. A total of four watermolecules are shown in this area of the active site to be includedwithin the crystal structure, two of which are shown to be participatingin hydrogen bonding with one or more atoms of the compound (2018)compound, or as a bridging water molecule between particular compound(2018) compound atoms and MASP-2 amino acid residue atoms. A sulfate ionis also present in the crystal structure and interacts with amidenitrogen N6 of compound (2018) as a hydrogen bond acceptor.

FIG. 23 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1149) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1149) atomsand the MASP-2 amino acid residue atoms. As shown therein, an amidinenitrogen N1 interacts with a carboxylate oxygen OD2 of ASP 627 as ahydrogen bond donor. The other amidine nitrogen N2 interacts with thecarbonyl oxygen O of SER 657 as a hydrogen bond donor and can interactwith a hydroxyl oxygen OG of SER 657 as a hydrogen bond donor, or withthe sulfur atom SG of CYS 660 as a hydrogen bond donor. The amidenitrogen N3 interacts with carbonyl oxygen O of SER 654 as a hydrogenbond donor. The carbonyl oxygen O2 interacts with a nitrogen atom of GLY656 as a hydrogen bond acceptor. In addition, one water molecule isshown to be included within the crystal structure in this area of theactive site, which participates in hydrogen bonding with the carbonyloxygen O1 of the compound (1149).

FIG. 24 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1031) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1031) and theMASP-2 amino acid residue atoms. The carbonyl oxygen O04 interacts witha guanidine nitrogen NE of ARG 630 as a hydrogen bond acceptor. Thecarbonyl oxygen O09 interacts with a guanidine nitrogen NH1 of ARG 630as a hydrogen bond acceptor. The amino group nitrogen N11 interacts witha carbonyl oxygen O of GLY 656 as a hydrogen bond donor.

FIG. 25 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1153) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1153)compound atoms and the MASP-2 amino acid residue atoms. As showntherein, an amidine nitrogen N1 interacts with a carbonyl oxygen O ofSER 657 as a hydrogen bond donor and with a carboxylate oxygen OD2 ofASP 627 as a hydrogen bond donor. The other amidine nitrogen N2interacts with a hydroxyl oxygen OG of SER 628 as a hydrogen bond donor.The carbonyl oxygen O1 interacts with guanidine nitrogen NH2 of ARG 630as a hydrogen bond acceptor. The amine nitrogen N5 interacts with acarbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygenO2 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, one water molecule is shown to be included withinthe crystal structure in this area of the active site, whichparticipates in hydrogen bonding with amide nitrogen N3 of the compound(1153).

FIG. 26 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1025) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1025) atomsand the MASP-2 amino acid residue atoms. Amine nitrogen N09 interactswith carboxylate oxygen OD2 of ASP 627 as a hydrogen bond donor and alsowith a carbonyl oxygen O of SER 628 as a hydrogen bond donor. Thepyridine nitrogen N05 also interacts with carbonyl oxygen O of SER 628as a hydrogen bond donor.

FIG. 27 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1012) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1012) atomsand the MASP-2 amino acid residue atoms. As shown therein, an aminenitrogen N5 interacts with a carboxylate oxygen OD2 of ASP 627 as ahydrogen bond donor and also with a carbonyl oxygen O of SER 657 as ahydrogen bond donor. The amide nitrogen N3 interacts with a carbonyloxygen of SER 654 as a hydrogen bond donor. The pyrrolidine nitrogen N1interacts with a carbonyl oxygen of GLY 656 as a hydrogen bond donor.The carbonyl oxygen O1 interacts with a nitrogen atom of GLY 656 as ahydrogen bond acceptor. In addition, a total of eleven water moleculesare shown in this area of the active site to be included within thecrystal structure, three of which are shown to be participating inhydrogen bonding, either with one or more atoms of the compound (1012),or as a bridging water molecule between particular compound (1012) atomsand MASP-2 amino acid residue atoms. One of the water atoms forms abridge between the pyridine nitrogen N4 and the carboxylate carbon OD1of ASP 627 and the hydroxyl oxygen OG of SER 628. A chloride ion is alsopresent in the crystal structure, bridging N1 of compound (1012) to NH2of ARG630 and a water molecule 141.

FIG. 28 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1078) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1078) atomsand the MASP-2 amino acid residue atoms. The carbonyl oxygen O2interacts with a guanidine nitrogen NH2 of ARG 630 as a hydrogen bondacceptor. The amide nitrogen N2 also interacts with the guanidinenitrogen NH2 of ARG 630, but as a hydrogen bond donor. The amidenitrogen N1 interacts with carbonyl oxygen O of SER 654 as a hydrogenbond donor. The carbonyl oxygen O1 interacts with a nitrogen N of GLY656 as a hydrogen bond acceptor.

FIG. 29 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1145) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1145)compound atoms and the MASP-2 amino acid residue atoms. As showntherein, an amidine nitrogen N5 interacts with a carbonyl oxygen O ofSER 657 as a hydrogen bond donor. The other amidine nitrogen N4interacts with a carbonyl oxygen O of SER 628 as a hydrogen bond donor.Amide nitrogen N1 interacts with carbonyl oxygen atom O of SER 654 as ahydrogen bond donor. The amine nitrogen N3 interacts with a carbonyloxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygen O2interacts with a nitrogen atom of GLY 656 as a hydrogen bond acceptor.In addition, two water molecules are shown to be included within thecrystal structure in this area of the active site, which participates inhydrogen bonding with the phenolic hydroxyl O1 and amide nitrogen N2 ofthe compound (1145).

FIG. 30 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1050) through hydrogen bonds. As shown therein, fourdifferent hydrogen bonds are present between the compound (1050) atomsand the MASP-2 amino acid residue atoms. As shown therein, an amidinenitrogen N4 interacts with a carbonyl oxygen O of SER 657 as a hydrogenbond donor. The amide nitrogen N2 interacts with a carbonyl oxygen O ofSER 654 as a hydrogen bond donor. The amino group nitrogen N5 interactswith a carbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyloxygen O2 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, three water molecules are shown to be includedwithin the crystal structure in this area of the active site, each ofwhich participate in hydrogen bonding with the compound (1050).

FIG. 31 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1253) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1253) atomsand the MASP-2 amino acid residue atoms. Amine nitrogen N07 interactswith carboxylate oxygen OD2 of ASP 627 as a hydrogen bond donor and alsowith a carbonyl oxygen O of SER 657 as a hydrogen bond donor. Thepyridine nitrogen N01 may interact with carbonyl oxygen O of SER 628 asa hydrogen bond donor and is in H-bonding distance to a water molecule16 which it may interact with as an acceptor or donor. Amide nitrogenN10 interacts with carbonyl oxygen O of SER 654 as a hydrogen bonddonor. Piperidine nitrogen N22 interacts with carbonyl oxygen O of GLY656 as a hydrogen bond donor. Carbonyl oxygen O17 interacts with anitrogen N of GLY 656 as a hydrogen bond acceptor. Six water moleculesare shown to be included within the crystal structure in this area ofthe active site, four of which are involved in hydrogen bonding, eitherwith one or more atoms of the compound (1253), or as a bridging watermolecule between particular compound (1253) atoms and MASP-2 amino acidresidue atoms.

FIG. 32 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1257) through hydrogen bonds. As shown therein, fourdifferent hydrogen bonds are present between the compound (1257)compound atoms and the MASP-2 amino acid residue atoms. As showntherein, an amine nitrogen N08 interacts with a carbonyl oxygen O of SER657 as a hydrogen bond donor. The pyridine nitrogen N01 may interactwith carbonyl oxygen O of SER 628 as a hydrogen bond donor and is inH-bonding distance to a water molecule which it may interact with as anacceptor or donor. The amide nitrogen N10 interacts with a carbonyloxygen of SER 654 as a hydrogen bond donor. The pyrrolidine nitrogen N18interacts with a carbonyl oxygen of GLY 656 as a hydrogen bond donor. Inaddition, a total of thirteen water molecules are shown in this area ofthe active site to be included within the crystal structure, four ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1257), or as a bridging water moleculebetween particular compound (1257) atoms and MASP-2 amino acid residueatoms

FIG. 33 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1297) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1297) atomsand the MASP-2 amino acid residue atoms. The amino group nitrogen N5interacts with a carboxyl group oxygen OD2 of ASP 627 as a hydrogen bonddonor and also with a carbonyl group oxygen O of SER 657 as a hydrogenbond donor. The pyridine nitrogen N4 interacts with a carbonyl oxygen Oof SER 628 as a hydrogen bond donor. The amide nitrogen N3 interactswith a carbonyl oxygen of SER 654 as a hydrogen bond donor. Thepiperidine nitrogen N1 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with a nitrogenatom of GLY 656 as a hydrogen bond acceptor. In addition, a total offour water molecules are shown in this area of the active site to beincluded within the crystal structure, which are shown to beparticipating in hydrogen bonding, either with one or more atoms of thecompound (1297), or as a bridging water molecule between particularcompound (1297) atoms and MASP-2 amino acid residue atoms.

FIG. 34 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1304) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1304) atomsand the MASP-2 amino acid residue atoms. An amine nitrogen N5 interactswith a carboxyl group oxygen OD2 of ASP 627 as a hydrogen bond donor andalso with a carbonyl oxygen O of SER 657 as a hydrogen bond donor. Thepyridine nitrogen N4 may interact with carbonyl oxygen O of SER 628 as ahydrogen bond donor and is in H-bonding distance to a water moleculewhich it may interact with as an acceptor or donor. The amide nitrogenN3 interacts with a carbonyl oxygen of SER 654 as a hydrogen bond donor.The pyrrolidine nitrogen N2 interacts with a carbonyl oxygen of GLY 656as a hydrogen bond donor. The carbonyl oxygen O1 interacts with anitrogen atom of GLY 656 as a hydrogen bond acceptor. In addition, atotal of eleven water molecules are shown to be included within thecrystal structure in this area of the active site, three of which areshown to be participating in hydrogen bonding, either with one or moreatoms of the compound (1304), or as a bridging water molecule betweenparticular compound (1304) atoms and MASP-2 amino acid residue atoms. Achloride ion is also present in the crystal structure in this area ofthe active site, which interacts with the pyrrolidine nitrogen N2 as ahydrogen bond acceptor.

FIG. 35 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1306) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1306) atomsand the MASP-2 amino acid residue atoms. As shown therein, one of theamidine nitrogens, N5, interacts with a carbonyl oxygen of SER 657 as ahydrogen bond donor and the other amidine nitrogen N4 interacts with acarbonyl group oxygen of SER 628 as a hydrogen bond donor and with acarboxyl group oxygen OD2 of ASP 627 as a hydrogen bond donor. Thepyrrolidine nitrogen N2 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with a nitrogenatom of GLY 656 as a hydrogen bond acceptor.

FIG. 36 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1307) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1307) atomsand the MASP-2 amino acid residue atoms. The amide nitrogen N3 interactswith a carbonyl oxygen of SER 654 as a hydrogen bond donor. Thepyrrolidine nitrogen N2 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with a nitrogenatom of GLY 656 as a hydrogen bond acceptor. Two water molecules areshown to be included within the crystal structure in this area of theactive site, both of which are shown to be participating in hydrogenbonding, either with one or more atoms of the compound (1307), or as abridging water molecule between particular compound (1307) atoms andMASP-2 amino acid residue atoms. The phenolic oxygen atom forms anintramolecular H-bond with O2 serving as an H-bond donor and itinteracts as a hydrogen bond acceptor with a water molecule that furtherinteracts with a nitrogen atom NH1 of ARG 630 as a hydrogen bondacceptor and a carbonyl oxygen of SER 657 as a hydrogen bond donor.

FIG. 37 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1328) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1328) atomsand the MASP-2 amino acid residue atoms. The amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donor.The pyridine nitrogen N4 interacts with a carbonyl oxygen O of SER 628as a hydrogen bond donor. The amide nitrogen N3 interacts with acarbonyl oxygen of SER 654 as a hydrogen bond donor. The pyrrolidinenitrogen N2 interacts with a carbonyl oxygen of GLY 656 as a hydrogenbond donor. The carbonyl oxygen O1 interacts with a nitrogen atom of GLY656 as a hydrogen bond acceptor. In addition, one water molecule isshown in this area of the active site to be included within the crystalstructure in this area of the active site, which participates inhydrogen bonding with the pyrrolidine nitrogen (N2) of the compound(1328).

FIG. 38 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1334) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1334) atomsand the MASP-2 amino acid residue atoms. The amide nitrogen N3 interactswith a carbonyl oxygen of SER 654 as a hydrogen bond donor. Thepyrrolidine nitrogen N2 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with a nitrogenatom of GLY 656 as a hydrogen bond acceptor. Nine water molecules areshown to be included within the crystal structure in this area of theactive site, five of which are shown to be participating in hydrogenbonding, either with one or more atoms of the compound (1334), or as abridging water molecule between particular compound (1334) atoms andMASP-2 amino acid residue atoms.

FIG. 39 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1335) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1335) atomsand the MASP-2 amino acid residue atoms. An amidine nitrogen N6interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with an amide group carbonyl oxygen OE1 of GLN 665 as a hydrogenbond donor. The other amidine nitrogen N5 interacts with a hydroxylgroup oxygen OG of SER 628 as a hydrogen bond donor. The amide nitrogenN1 interacts with a carbonyl oxygen of SER 654 as a hydrogen bond donor.The amino group nitrogen N3 interacts with a carbonyl oxygen of GLY 656as a hydrogen bond donor. The carbonyl oxygen O1 interacts with anitrogen atom of GLY 656 as a hydrogen bond acceptor. In addition, fourwater molecules are shown in this area of the active site to be includedwithin the crystal structure, three of which are shown to beparticipating in hydrogen bonding, either with one or more atoms of thecompound (1335), or as a bridging water molecule between particularcompound (1335) atoms and MASP-2 amino acid residue atoms.

FIG. 40 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1338) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1338) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carboxyl group oxygen OD2 of ASP 627 as a hydrogen bonddonor and also with a carbonyl oxygen O of SER 657 as a hydrogen bonddonor. The pyridine nitrogen N4 may interact with carbonyl oxygen O ofSER 628 as a hydrogen bond donor and is in H-bonding distance to a watermolecule which it may interact with as an acceptor or donor. The amidenitrogen N3 interacts with a carbonyl oxygen of SER 654 as a hydrogenbond donor. The pyrrolidine nitrogen N2 interacts with a carbonyl oxygenof GLY 656 as a hydrogen bond donor. The carbonyl oxygen O1 interactswith a nitrogen atom of GLY 656 as a hydrogen bond acceptor. Inaddition, a total of seventeen water molecules are shown to be includedwithin the crystal structure in this area of the active site, three ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1338), or as a bridging water moleculebetween particular compound 1338 atoms and MASP-2 amino acid residueatoms.

FIG. 41 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1345) through hydrogen bonds. As shown therein, sevendifferent hydrogen bonds are present between the compound (1345) atomsand the MASP-2 amino acid residue atoms. An amidine nitrogen N6interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carbonyl oxygen OE1 of GLN 665 as a hydrogen bond donor. Theother amidine nitrogen N5 interacts with a carbonyl oxygen O of SER 628as a hydrogen bond donor. The amide nitrogen N1 interacts with acarbonyl oxygen O of SER 654 as a hydrogen bond donor. The secondaryamine nitrogen N3 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with guanidinenitrogen NH1 of ARG 630 as a hydrogen bond acceptor. The carbonyl oxygenO2 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, one water molecule is shown to be included withinthe crystal structure in this area of the active site, whichparticipates in hydrogen bonding as a hydrogen bond donor with carbonyloxygen O3 of the compound (1345).

FIG. 42 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1351) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1351) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carboxylate group oxygen OD2 of ASP 627 as a hydrogenbond donor and also with a carbonyl oxygen O of SER 657 as a hydrogenbond donor. The amide nitrogen N3 interacts with a carbonyl oxygen ofSER 654 as a hydrogen bond donor. The pyrrolidine nitrogen N2 interactswith a carbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyloxygen O1 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, a total of eight water molecules are shown to beincluded within the crystal structure in this area of the active site,five of which are shown to be participating in hydrogen bonding, eitherwith one or more atoms of the compound (1351), or as a bridging watermolecule between particular compound (1351) atoms and MASP-2 amino acidresidue atoms.

FIG. 43 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1353) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1353) atomsand the MASP-2 amino acid residue atoms. As shown therein, an aminogroup nitrogen N5 interacts with a carboxylate group oxygen OD2 of ASP627 as a hydrogen bond donor and also with a carbonyl oxygen O of SER657 as a hydrogen bond donor. The amide nitrogen N3 interacts with acarbonyl oxygen of SER 654 as a hydrogen bond donor. The piperidinenitrogen N1 interacts with a carbonyl oxygen of GLY 656 as a hydrogenbond donor. The carbonyl oxygen O1 interacts with a nitrogen atom of GLY656 as a hydrogen bond acceptor. A total of thirteen water molecules areshown to be included within the crystal structure in this area of theactive site, four of which are shown to be participating in hydrogenbonding, either with one or more atoms of the compound (1353), or as abridging water molecule between particular compound (1353) atoms andMASP-2 amino acid residue atoms. In addition, a chloride ion is present,which interacts with the piperidine nitrogen N1 as a hydrogen bondacceptor. A sulfate ion is also present.

FIG. 44 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1360) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1360) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carboxylate group oxygen OD2 of ASP 627 as a hydrogenbond donor and also with a carbonyl oxygen O of SER 657 as a hydrogenbond donor. The amide nitrogen N3 interacts with a carbonyl oxygen ofSER 654 as a hydrogen bond donor. The pyridine nitrogen N4 interactswith a carbonyl oxygen of SER 628 as a hydrogen bond donor, and is inH-bonding distance to a water molecule which it may interact with as anacceptor or donor. The pyrrolidine nitrogen N2 interacts with a carbonyloxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygen O1interacts with a nitrogen atom of GLY 656 as a hydrogen bond acceptor.In addition, a total of seven water molecules are shown to be includedwithin the crystal structure in this area of the active site, four ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1360), or as a bridging water moleculebetween particular compound (1360) atoms and MASP-2 amino acid residueatoms. A sulfate ion and a chloride ion is also present.

FIG. 45 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1367) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1367) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N4interacts with a carboxylate group oxygen OD2 of ASP 627 as a hydrogenbond donor and also with a carbonyl oxygen O of SER 657 as a hydrogenbond donor. The pyridine nitrogen N3 may interact with carbonyl oxygen Oof SER 628 as a hydrogen bond donor and is in H-bonding distance to awater molecule which it may interact with as an acceptor or donor. Theamide nitrogen N2 interacts with a carbonyl oxygen of SER 654 as ahydrogen bond donor. The pyrazole nitrogen N6 interacts with a carbonyloxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygen O2interacts with a nitrogen atom of GLY 656 as a hydrogen bond acceptor.In addition, a total of seven water molecules are to be included withinthe crystal structure shown in this area of the active site, three ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1367), or as a bridging water moleculebetween particular compound (1367) atoms and MASP-2 amino acid residueatoms.

FIG. 46 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1368) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1368) atomsand the MASP-2 amino acid residue atoms. As shown therein, an aminogroup nitrogen N38 interacts with a carbonyl oxygen O of SER 657 as ahydrogen bond donor and also with a carboxyl group oxygen OD2 of ASP 627as a hydrogen bond donor. The pyridine nitrogen N34 may interact withcarbonyl oxygen O of SER 628 as a hydrogen bond donor and is inH-bonding distance to a water molecule which it may interact with as anacceptor or donor. The amide nitrogen N01 interacts with a carbonyloxygen of SER 654 as a hydrogen bond donor. The carbonyl oxygen O29interacts with a nitrogen of GLY 656 as a hydrogen bond acceptor. Theacetamide group nitrogen N17 interacts with a carbonyl oxygen of PRO 606as a hydrogen bond donor. In addition, a total of fifteen watermolecules are shown in this area of the active site to be includedwithin the crystal structure, five of which are shown to beparticipating in hydrogen bonding, either with one or more atoms of thecompound (1368), or as a bridging water molecule between particularcompound (1368) atoms and MASP-2 amino acid residue atoms. A sulfate ionis also present.

FIG. 47 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1371) through hydrogen bonds. As shown therein, fourdifferent hydrogen bonds are present between the compound (1371) atomsand the MASP-2 amino acid residue atoms. The amide nitrogen N3 interactswith a carbonyl oxygen of SER 654 as a hydrogen bond donor. Thepyrrolidine nitrogen N2 interacts with a carbonyl oxygen of GLY 656 as ahydrogen bond donor. The carbonyl oxygen O1 interacts with a nitrogenatom of GLY 656 as a hydrogen bond acceptor. A tetrazole nitrogen N7interacts with a water molecule as a hydrogen bond acceptor. C23interacts with a carbonyl oxygen O of SER657 as a hydrogen bond donor.One water molecule is shown in this area of the active site to beincluded within the crystal structure, which participates in hydrogenbonding with tetrazole nitrogen N6 of the compound (1371).

FIG. 48 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1372) through hydrogen bonds. As shown therein, eightdifferent hydrogen bonds are present between the compound (1372) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N4interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxyl group oxygen atom O2 of ASP 627 as a hydrogen bonddonor. The pyridine nitrogen N3 may interact with carbonyl oxygen O ofSER 628 as a hydrogen bond donor and is in H-bonding distance to a watermolecule which it may interact with as an acceptor or donor. The amidenitrogen N2 interacts with a carbonyl oxygen of SER 654 as a hydrogenbond donor. The pyrrolidine nitrogen N5 interacts with a carbonyl oxygenof GLY 656 as a hydrogen bond donor. The carbonyl oxygen O2 interactswith a nitrogen atom of GLY 656 as a hydrogen bond acceptor. Inaddition, a total of eight water molecules are shown to be includedwithin the crystal structure in this area of the active site, four ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1372), or as a bridging water moleculebetween particular compound (1372) atoms and MASP-2 amino acid residueatoms. A sulfate ion is also present.

FIG. 49 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1373) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1373) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxylate group oxygen atom OD2 of ASP 627 as a hydrogenbond donor. The pyridine nitrogen N3 may interact with carbonyl oxygen Oof SER 628 as a hydrogen bond donor and is in H-bonding distance to awater molecule which it may interact with as an acceptor or donor. Theamide nitrogen N3 interacts with a carbonyl oxygen of SER 654 as ahydrogen bond donor. The pyrrolidine nitrogen N2 interacts with acarbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygenO1 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, a total of seventeen water molecules are shown inthis area of the active site to be included within the crystalstructure, three of which are shown to be participating in hydrogenbonding, either with one or more atoms of the compound (1373), or as abridging water molecule between particular compound (1373) atoms andMASP-2 amino acid residue atoms. Chloride and sulfate ions are alsopresent.

FIG. 50 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1492) through hydrogen bonds. As shown therein, sevendifferent hydrogen bonds are present between the compound (1492) atomsand the MASP-2 amino acid residue atoms. A benzimidazole nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donor.A benzimidazole nitrogen ND6 interacts with a carboxyl group oxygen atomOD1 of ASP 627 as a hydrogen bond donor. An amino group nitrogen N7interacts with a carboxyl group oxygen atom OD2 of ASP 627 as a hydrogenbond donor and also with a carbonyl oxygen atom O of GLN 665 as ahydrogen bond donor. The amide nitrogen N4 interacts with a carbonyloxygen of SER 654 as a hydrogen bond donor. The nitrogen N3 interactswith a carbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyloxygen O1 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor.

FIG. 51 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1399) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1399) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxylate oxygen atom OD2 of ASP 627 as a hydrogen bonddonor. The pyridine nitrogen N4 may interact with carbonyl oxygen O ofSER 628 as a hydrogen bond donor and is in H-bonding distance to a watermolecule which it may interact with as an acceptor or donor. The amidenitrogen N3 interacts with a carbonyl oxygen of SER 654 as a hydrogenbond donor. The pyrrolidine nitrogen N1 interacts with a carbonyl oxygenof GLY 656 as a hydrogen bond donor. The carbonyl oxygen O1 interactswith a nitrogen atom of GLY 656 as a hydrogen bond acceptor. Inaddition, a total of eleven water molecules are shown in this area ofthe active site to be included within the crystal structure, four ofwhich are shown to be participating in hydrogen bonding, either with oneor more atoms of the compound (1399), or as a bridging water moleculebetween particular compound (1399) atoms and MASP-2 amino acid residueatoms. Chloride and sulfate ions are also present and shown to beinteracting in hydrogen bonding with water in the crystal structure.

FIG. 52 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1406) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1406) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxyl group oxygen atom OD2 of ASP 627 as a hydrogen bonddonor. The amide nitrogen N3 interacts with a carbonyl oxygen of SER 654as a hydrogen bond donor. The pyrrolidine nitrogen N2 interacts with acarbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygenO1 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, a total of eight water molecules are shown inthis area of the active site to be included within the crystalstructure, four of which are shown to be participating in hydrogenbonding, either with one or more atoms of the compound (1406), or as abridging water molecule between particular compound (1406) atoms andMASP-2 amino acid residue atoms.

FIG. 53 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1411) through hydrogen bonds. As shown therein, sixdifferent hydrogen bonds are present between the compound (1411) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxyl group oxygen atom OD2 of ASP 627 as a hydrogen bonddonor. The pyridine nitrogen N4 may interact with carbonyl oxygen O ofSER 628 as a hydrogen bond donor and is in H-bonding distance to a watermolecule which it may interact with as an acceptor or donor. The amidenitrogen N1 interacts with a carbonyl oxygen of SER 654 as a hydrogenbond donor. The carbonyl oxygen O2 interacts with a nitrogen atom of GLY656 as a hydrogen bond acceptor. The carboxylate oxygen O3 interactswith a guanidine nitrogen NH2 of ARG 630 as a hydrogen bond acceptor. Inaddition, a total of four water molecules are shown in this area of theactive site to be included within the crystal structure, three of whichare shown to be participating in hydrogen bonding, either with one ormore atoms of the compound (1411), or as a bridging water moleculebetween particular compound (1411) atoms and MASP-2 amino acid residueatoms.

FIG. 54 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1433) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1433) atomsand the MASP-2 amino acid residue atoms. Amide nitrogen N3 interactswith carbonyl oxygen O of SER 654 as a hydrogen bond donor. Piperidinenitrogen N5 interacts with carbonyl oxygen O of GLY 656 as a hydrogenbond donor. Carbonyl oxygen O2 interacts with a nitrogen N of GLY 656 asa hydrogen bond acceptor. Six water molecules are shown to be includedwithin the crystal structure in this area of the active site, four ofwhich are involved in hydrogen bonding, either with one or more atoms ofthe compound (1433), or as a bridging water molecule between particularcompound (1433) atoms and MASP-2 amino acid residue atoms.

FIG. 55 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1435) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1435) atomsand the MASP-2 amino acid residue atoms. The amino group nitrogen N5interacts with carboxylate oxygen OD2 of ASP 627 as a hydrogen bonddonor and with carbonyl oxygen O of SER 657 as a hydrogen bond donor.The amide nitrogen N3 interacts with a carbonyl oxygen of SER 654 as ahydrogen bond donor. The pyrrolidine nitrogen N2 interacts with acarbonyl oxygen of GLY 656 as a hydrogen bond donor. The carbonyl oxygenO1 interacts with a nitrogen atom of GLY 656 as a hydrogen bondacceptor. In addition, eight water molecules are shown in this area ofthe active site to be included within the crystal structure in this areaof the active site, three of which are involved in hydrogen bonding,either with one or more atoms of the compound (1435), or as a bridgingwater molecule between particular compound (1435) atoms and MASP-2 aminoacid residue atoms. A chloride ion is also present, which mayparticipate in hydrogen bonding with the pyrrolidine nitrogen N2.

FIG. 56 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1441) through hydrogen bonds. As shown therein, fivedifferent hydrogen bonds are present between the compound (1441) atomsand the MASP-2 amino acid residue atoms. An amino group nitrogen N5interacts with a carbonyl oxygen O of SER 657 as a hydrogen bond donorand with a carboxyl group oxygen atom OD2 of ASP 627 as a hydrogen bonddonor. The pyridine nitrogen N4 may interact with carbonyl oxygen O ofSER 628 as a hydrogen bond donor and is in H-bonding distance to a watermolecule which it may interact with as an acceptor or donor. The amidenitrogen N1 interacts with a carbonyl oxygen of SER 654 as a hydrogenbond donor. The carbonyl oxygen O1 interacts with a nitrogen atom of GLY656 as a hydrogen bond acceptor. In addition, a total of twelve watermolecules are shown in this area of the active site to be includedwithin the crystal structure, three of which are shown to beparticipating in hydrogen bonding, either with one or more atoms of thecompound (1441), or as a bridging water molecule between particularcompound (1441) atoms and MASP-2 amino acid residue atoms.

FIG. 57 is an illustration of MASP-2 CCP2-SP amino acid interactionswith compound (1450) through hydrogen bonds. As shown therein, threedifferent hydrogen bonds are present between the compound (1450) atomsand the MASP-2 amino acid residue atoms. Amide nitrogen N3 interactswith carbonyl oxygen O of SER 654 as a hydrogen bond donor. Pyrrolidinenitrogen N2 interacts with carbonyl oxygen O of GLY 656 as a hydrogenbond donor. Carbonyl oxygen O1 interacts with a nitrogen N of GLY 656 asa hydrogen bond acceptor. Nine water molecules are shown to be includedwithin the crystal structure in this area of the active site, three ofwhich are involved in hydrogen bonding, either with one or more atoms ofthe compound (1450), or as a bridging water molecule between particularcompound (1450) atoms and MASP-2 amino acid residue atoms. A chlorideion is also present, which participates in hydrogen bonding with thepyrrolidine nitrogen atom N2.

In certain aspects, the present disclosure provides a compound withMASP-2 inhibitory activity, for therapeutic use in the treatment of aMASP-2-associated disease or disorder, wherein the compound has one ormore such as 1, 2, 3, 4, or 5 of the following interactions (a) to (e):

a) the compound binds via H-bonds with one or more of PRO 606, ASP 627,SER 628, ARG 630, SER 633, SER 654, GLY 656, SER 657, CYS 660 and GLN665 in MASP-2;

b) the compound binds via ionic or electrostatic interactions orhydrogen bonding to one or more of ASP 627 and ARG 630 in MASP-2;

c) the compound interacts via a water molecule in MASP-2 to one or moreof TYR 602, TYR 607, ASP 627, SER 628, SER 657, ASN 659, GLU 662, TRP655, GLY656, CYS660, GLN 665, TYR 666, VAL 668, and ARG 630 in MASP-2;

d) the compound interacts via π-π interactions with one or more of PHE529, TYR 607, and TRP 655 in MASP-2; and

e) the compound interacts via van der Waals contacts to one or more ofALA 468, ALA 469, HIS 483, ASP 526, ALA 527, GLY 528, PHE 529, LEU 575,PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS 629, ARG 630,GLY 631, ASP 632, SER 633, GLY 634, GLY 635, VAL 653, SER 654, TRP 655,GLY656, SER 657, MET 658, ASN 659, CYS 660, GLN 665, GLY 667, and TYR669 in MASP-2,

wherein the compound is not an endogenous MASP-2 ligand or substrate.

In certain aspects, the present disclosure provides a compound withMASP-2 inhibitory activity, for therapeutic use in the treatment of aMASP-2-associated disease or disorder, wherein the compound has one ormore such as 1, 2, 3, 4, or 5 of the following interactions (a) to (e):

a) the compound binds via H-bonds with 1, 2, 3, 4, 5, 6 or 7 of PRO 606,ARG 630, SER 633, SER 654, SER 657, CYS 660 and GLN 665 in MASP-2;

b) the compound interacts via van der Waals contacts to 1, 2, 3, 4, 5,6, 7 or 8 of ALA 469, GLY 634, GLY 635, SER 657, ASN 659, CYS 660, GLN665, and TYR 669 in MASP-2.

Protein Data Bank access code 3TVJ). The following MASP-2 residues wereidentified to bind to peptide SGMI-2 via hydrogen bonds: GLY 656(2H-bonds), ASP 627, SER 628 (2H-bonds), SER 633 (2H-bonds), GLY 631,THR 467 (3H-bonds), GLY 464, GLY 465, MET 658 and via van der Waalsinteractions with PRO 608, PHE 529, TYR 602, TYR 607, TRP 655, HIS 483,ALA 484, VAL 653, LEU 575, LEU 581, ALA 468, THR 466 and ARG 630. Ananalysis of the associated structure 3TVJ with LigPlot Plus produced thefollowing amino acids being involved in non-bonded contacts: GLY 464,GLY 465, THR 466, THR 467, ALA 468, HIS 483, ALA 484, HIS 525, ASP 526,ALA 527, GLY 528, PHE 529, LEU 575, LEU 581, TYR 602, PRO 606, TYR 607,PRO 608, ARG 609, GLY 610, SER 611, ASP 627, SER 628, CYS 629, ARG 630,GLY 631, ASP 632, SER 633, VAL 653, SER 654, TRP655, GLY 656, MET 658,GLY 667.

In certain aspects, the present disclosure provides a compound withMASP-2 inhibitory activity, for therapeutic use in the treatment of aMASP-2-associated disease or disorder, wherein the compound has one ormore such as 1, 2, 3, 4, or 5 of the following interactions (a) to (e):

a) the compound binds via H-bonds with one or more of ASP 627, SER 628,SER 654, GLY 656, GLN 665, and SER 657 in MASP-2;

b) the compound binds via ionic or electrostatic interactions orhydrogen bonding to ASP 627 in MASP-2;

c) the compound interacts via a water molecule in MASP-2 to one or moreof ASP 627, GLN 665, SER 657, ASN 659, SER 628, GLU 662, VAL 668,TYR607, TYR602, ARG630 in MASP-2;

d) the compound interacts via π-π interactions with one or more of PHE529, TYR 607, and TRP 655 in MASP-2; and

e) the compound interacts via van der Waals contacts to one or more ofHIS 483, PHE 529, PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628,CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER 657,MET 658, ASN 659, CYS 660, GLN 665, GLY 667 and TYR 669 in MASP-2,

wherein the compound is not an endogenous MASP-2 ligand or substrate.

In certain aspects, the compound interacts with 1, 2, 3, 4, or 5 of thefeatures (a) to (e) above in any combination. The compound is not anendogenous MASP-2 ligand or substrate.

In some embodiments, the compound binds via H-bonds with one or more ofthe following: PRO 606, ASP 627, SER 628, SER 633, SER 654, GLY 656, SER657, CYS 660 and GLN 665 in MASP-2.

In some embodiments, the compound binds via H-bonds with one or more ofthe following: ASP 627, SER 628, SER 654, GLY 656, GLN 665 and SER 657in MASP-2.

In some embodiments, the compound binds via 1-10H-bonds.

In some embodiments, the compound binds via 3H-bonds to SER 654 and GLY656, wherein there are two H-bonds to GLY 656 in MASP-2.

In some embodiments, the compound binds via ionic or electrostaticinteractions or hydrogen bonding to one or both of ASP 627 and ARG 630in MASP-2.

In some embodiments, the compound binds via ionic or electrostaticinteractions or hydrogen bonding to ASP 627 in MASP-2.

In some embodiments, the compound does not bind via ionic interactionsto ASP 627 or ARG 630 in MASP-2.

In some embodiments, the compound does not bind via ionic interactionsto ASP 627 in MASP-2.

In some embodiments, the compound binds via a water molecule in MASP-2to one or more of TYR 602, TYR 607, ASP 627, SER 628, SER 657, ASN 659,GLU 662, TRP 655, GLY656, CYS660, GLN 665, TYR 666, VAL 668, and ARG 630in MASP-2.

In some embodiments, the compound binds via a water molecule in MASP-2to one or more of ASP 627, GLN 665, SER 657, ASN 659, SER 628, GLU 662,VAL 668, TYR 607, TYR 602, and ARG 630.

In some embodiments, the compound binds via 1-20 water molecule(s) inMASP-2.

In some embodiments, the compound binds via 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, or 17 water molecule(s) in MASP-2.

In some embodiments, the compound interacts via π-π interactions withone or more of PHE 529, TYR 607, and TRP 655 in MASP-2.

In some embodiments, the compound interacts via van der Waals contactsto one or more of ALA 468, ALA 469, HIS 483, ASP 526, ALA 527, GLY 528,PHE 529, LEU 575, PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628,CYS 629, ARG 630, GLY 631, ASP 632, SER 633, GLY634, GLY 635, VAL 653,SER 654, TRP 655, GLY 656, SER 657, MET 658, ASN 659, CYS 660, GLN 665,GLY 667, and TYR 669 in MASP-2.

In some embodiments, the compound interacts via van der Waals contactsto one or more of HIS 483, PHE 529, PRO 606, TYR 607, PRO 608, SER 611,ASP 627, SER 628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655,GLY 656, SER 657, MET 658, ASN 659, CYS 660, GLN 665, GLY 667 and TYR669 in MASP-2.

The foregoing set of rules for interactions was developed to increaseinhibition of MASP-2, while at the same time reducing inhibition ofthrombin. More specifically the above-described rules provide forcompounds that preferentially inhibit MASP-2 relative to inhibition ofthrombin. In certain aspects, the selectivity ratio of MASP-2:thrombinis at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1,8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1,20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

Crystallographic data and evidence aided in the development anddiscovery of the rules.

The foregoing ligand-MASP-2 atom contacts represent polar interactions.Ligand atom to MASP-2 atom polar contacts (hydrogen bonds and ionicbonding) are included for pair-wise distances with a maximum contactdistance of 3.35 Å between donor and acceptor atom as computed byLigPlot+ software settings for hydrogen-bond calculation parametersemploying models derived from the corresponding crystallographic MASP-2compound co-structures. MASP-2 amino acid residue numbering (MASP-2 AA#) is according to Uniprot accession code O00187, atom numbering foramino acids (AA atom) according to conventions established by theProtein Data Bank and atom ligand numbering assigned as depicted inFIGS. 1-57 . Table A1 (Appendix) illustrates interaction of ligandatoms, which are D for hydrogen bond donor, and A for hydrogen bondacceptor. Distance units are in Angstrom.

MASP-2 specific peptide inhibitors have been developed previously(Kocsis et al., 2010, Héja et al., 2012). Small molecule inhibitors withdrug-like characteristics, however, have not been reported in thepublished literature. The interaction of an artificially evolved MASP-2specific 38-mer polypeptide, named SGMI-2, with MASP-2 was determined bycrystallographic analysis (Héja et al., 2012, Protein Data Bank accesscode 3TVJ). The following MASP-2 residues were identified to bind topeptide SGMI-2 via hydrogen bonds: GLY 656 (2H-bonds), ASP 627, SER 628(2H-bonds), SER 633 (2H-bonds), GLY 631, THR 467 (3H-bonds), GLY 464,GLY 465, MET 658 and via van der Waals interactions with PRO 608, PHE529, TYR 602, TYR 607, TRP 655, HIS 483, ALA 484, VAL 653, LEU 575, LEU581, ALA 468, THR 466 and ARG 630. An analysis of the associatedstructure 3TVJ with LigPlot+ produced the following amino acids beinginvolved in non-bonded contacts: GLY 464, GLY 465, THR 466, THR 467, ALA468, HIS 483, ALA 484, HIS 525, ASP 526, ALA 527, GLY 528, PHE 529, LEU575, LEU 581, TYR 602, PRO 606, TYR 607, PRO 608, ARG 609, GLY 610, SER611, ASP 627, SER 628, CYS 629, ARG 630, GLY 631, ASP 632, SER 633, VAL653, SER 654, TRP655, GLY 656, MET 658, GLY 667. The interaction ofSGMI-2 with MASP-2 is reported to cause substantial distortions withinthe MASP-2 molecule and Héja et al. (2012) point out that such adistortion might cause an energy penalty, potentially weakening thebinding strength for MASP-2. (see, Divid Héja, Veronika Harmat,Krisztián Fodor, Matthias Wilmanns, József Dobó, Katalin A. Kékesi,Péter Závodszky, Péter Gál, Gábor Pál. Monospecific Inhibitors Show ThatBoth Mannan-binding Lectin-associated Serine Protease-1 (MASP-1) and -2Are Essential for Lectin Pathway Activation and Reveal StructuralPlasticity of MASP-2. Journal of Biological Chemistry 287, 20290-20300(2012) incorporated herein by reference).

In Table A2 (Appendix) ligand-MASP-2 atom contacts for van derWaals-type interactions between MASP-2 and compounds disclosed hereinare given. Ligand atom to MASP-2 atom contacts are included forpair-wise interactions with a minimum distance of 2.9 Å and a maximumcontact distance of 3.9 Å as computed by LigPlot+ software settings fornon-bonded contact parameters employing models derived from thecorresponding crystallographic MASP-2-compound co-structures. MASP-2amino acid residue numbering (MASP-2 AA #) is according to Uniprotaccession code O00187, atom numbering for amino acids (AA atom)according to conventions established by the Protein Data Bank and atomligand numbering assigned as depicted in FIGS. 1-18 . Distance units arein Angstrom.

In certain aspects, the compounds having MASP-2 inhibitory activity havea molecular weight of about 300 g/mol to about 600 g/mol, or about 350g/mol to about 550 g/mol, or about 350 to about 500 g/mol, such as about350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480,490 or about 500 g/mol. Typically, a small molecule has a molecularweight in these ranges.

In certain aspects, the present disclosure provides compounds that areselective for MASP-2 over thrombin. In other words, the compounds ofinterest have a greater affinity for MASP-2 (i.e., a smaller Ki forMASP-2) than the same compound for thrombin (i.e., the Ki for thrombinis larger). In certain aspects, the selectivity ratio of MASP-2:thrombinis at least 1.1:1, 1.25:1, 1.5:1, 1.75:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1,8:1, 9:1, 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1,20:1, 21:1, 22:1, 23:1, 24:1, 25:1, or 30:1.

As will be described in more detail, the active site for MASP-2 has a“V” shaped crevice, which allows for and accommodates a stericallylarger molecule. The V-shaped crevice of MASP-2, accepts ‘long’sterically bulky moieties such as a rotatable aromatic residue in theM₄-region of certain of the molecules of the disclosure.

As will be described in more detail, the active site for MASP-2 has a“S1 indentation”, which allows for and accommodates a sterically largermolecule. The S1 indentation of MASP-2, accepts ‘small’ moieties such asa methyl group in a chloroazaindole residue in the M1-region of certainof the molecules of the disclosure.

As will be described in more detail, the active site for MASP-2 has a“S2 shelf”, which allows for and accommodates a sterically largermolecule. The S2 shelf of MASP-2, accepts ‘large’ moieties such as aglutaminyl groups in the M3-region of certain of the molecules of thedisclosure.

As will be described in more detail, the active site for MASP-2 has a“S3 entry indentation”, which allows for and accommodates a stericallylarger molecule. The S3 entry indentation of MASP-2, accepts ‘planararomatic’ moieties such as a pyrazole ring connecting the M3 with the M4segments of certain of the molecules of the disclosure.

On the other hand, the backside of the active site in thrombin isclosed. Therefore, larger or bulky groups are not stericallyaccommodated in the same manner as thrombin due to this closure.Thrombin does not have a crevice in the active site. As such, bulkygroups in the M₄ region are not well accommodated.

Moreover, the crystallographic evidence indicates that key amino acidsmaking up the V shaped crevice of MASP-2 are one or more of thefollowing 6 amino acids: PHE 529, GLY 528, TRP 655, SER 611, PRO 608,TYR 607, PRO 606, such as 1, 2, 3, 4, 5, or all 6 amino acids.

In addition, it was discovered that thrombin possesses a ridge, creatinga barrier for large bulky residues (M₄) preventing occupation of thissite. The ridge includes the amino acids ASN 98, LEU 99, and ILE 174(defined using Protein Data Bank structure 1K22 numbering) or GLU130 andILE209 (defined using numbering of Protein Data Bank structure file4BAH). In the corresponding region in MASP-2 however, a crevice existsthat is lined by amino acids PHE 529, GLY 528, TRP 655, SER 611, PRO608, TYR 607, and PRO 606. As there is no corresponding barrier to largebulky residues in MASP-2, large bulky residues can bind and, provide ameans to design specificity for MASP-2 over thrombin or other similarproteases.

Based on crystallographic models, certain of the compounds of thisdisclosure have a specificity for binding to MASP-2 as compared tothrombin.

FIG. 58 to 63 show a region of the S3-S4 binding pockets of thrombin,compared to the S3-S4 binding pockets of MASP-2, with protein surfaceresidues depicted as a surface and the bound small molecules depicted asball and stick. FIG. 58 , FIG. 59 , FIG. 61 and FIG. 63 show a region ofthe S3-S4 binding pockets of thrombin, whereas the S3-S4 binding pocketsof MASP-2 are shown in FIG. 60 and FIG. 62 .

FIG. 58 depicts melagatran bound to thrombin (Protein Data Bankaccession code 4BAH) with its cyclohexyl group embedded in a pocket thatis lined by a ridge formed by GLU 130, ASN 131, ILE 209 and GLU 259. Thebenzamidine functional group of melagatran is located in a deep pocket(S1) of thrombin on the right-hand side of the image.

FIG. 59 shows melagatran bound to thrombin overlaid with a MASP-2selective compound (1065) bound to MASP-2. The overlay reproduces thelocation of the benzamidine function of both molecules (1065) bound toMASP-2 and melagatran bound to thrombin, and as shown, there is a clashwith the ridge formed by ASN 131 and ILE 209.

FIG. 60 is a plot showing compound (1065) bound to the SP domain ofMASP-2 with its bulky phenyl group fitting into a crevice that is formedby MASP-2 residues GLY 528 and PHE 529 on one side, and SER 611, PRO608, TYR 607 and PRO 606 on the opposite side.

FIG. 61 depicts compound (1334) bound to thrombin with its benzyl groupfolded back onto a surface that is lined by a ridge formed by GLU 259,and GLY 219. The chloroazaindole functional group of compound (1334) islocated in a deep pocket (S1) of thrombin on the right-hand side of theimage.

FIG. 62 illustrates compound (1334) bound to the SP domain of MASP-2with its bulky phenyl group fitting into a crevice that is formed byMASP-2 residues GLY 528 and PHE 529 on one side, and SER 611, PRO 608,TYR 607 and PRO 606 on the opposite side.

FIG. 63 is a plot showing the MASP-2 selective compound (1334) bound toMASP-2 overlaid with compound (1334) bound to thrombin. The overlayreproduces the location of the chloroazaindole function of the moleculecompound (1334) bound to MASP-2 and compound (1334) bound to thrombin.

The difference between the closed pocket in thrombin to the open crevicein MASP-2 provides a mechanism to design compounds with selectivity toMASP-2 over thrombin. For example, elongated and bulky moieties fit intothe MASP-2 crevice, but would clash with the ridge in thrombin.

FIGS. 64 and 65 illustrate a schematic depiction of selectivity forMASP-2 vs thrombin in region S3-S4, based on analysis ofcrystallographic models. FIG. 64 illustrates the S3-S4 binding pocketsof MASP-2, whereas FIG. 65 illustrates S3-S4 binding pockets ofthrombin. Both are shown with the protein in grey and the bound smallmolecules depicted as dark grey ellipsoids. As shown in FIG. 65 , inthrombin, only small moieties of M₄ (e.g. cyclohexyl groups) can fitinto a pocket formed by LEU99, ASN98, ILE174, GLU259, GLY219. FIG. 64shows a small molecule bound to the equivalent S3-S4 pocket in the SPdomain of MASP-2 that reaches further into a crevice formed by MASP-2residues GLY 528 and PHE 529 on one side, and SER 611, PRO 608, TYR 607and PRO 606 on the opposite side. Hence, larger molecules with elongatedand bulky groups in M₄ can fit into the crevice in MASP-2, but cannotbind to the small S3-S4 pocket in thrombin. FIG. 64 shows the opencrevice in MASP-2 provides a mechanism to design compounds withselectivity to MASP-2 over thrombin accommodating sterically bulkygroups in M₄.

Without being limited by any theory, based on the analysis of thestructures, structural features of the MASP-2 and thrombin and the waythat molecules interact with such features in MASP-2 and thrombin can beused to identify binding rules and structural features of compounds thatcontribute to selectivity for MASP-2 and thrombin.

S1-indentation: While not being limited by any theory, it is understoodthat the S1 pocket of MASP-2 may accept molecules of certain sizes andshapes that are unlikely to fit into the S1 pocket of thrombin. Thissite can be occupied, e.g., by moieties M₁ of compounds as describedherein. In fact, the S1 pocket of MASP-2 is lined with an amino acidsequence comprising GLY 656, SER 657, MET 658, ASN 659 and CYS 660. Thecorresponding sequence is shorter by one amino acid in thrombin(comprising the amino acids GLY 216, GLU 217, GLY 219 and Cys220,defined using Protein Data Bank structure 1K22 numbering). This sectionin MASP-2 forms a concave space in the S1 pocket, whereas in thrombinthere is less space, hence restricting the size of ligand molecules thatmay bind into the S1 pocket. Certain MASP-2 selective compounds werefound to form H-bonds and van der Waals contacts with surface liningresidues of the S1 pocket of MASP-2, including ASP 627, SER 628, CYS629, SER 633, TRP 655, GLY 656, SER 657, CYS 660, GLY 667, and TYR 669.Thus, it is understood that compounds having selectivity for inhibitingMASP-2 over thrombin can be compounds that make interactions with theamino acids lining the S-1 pocket of MASP-2. For example, the MASP-2selective inhibitors can include compounds that make, e.g., 1, 2, 3, 4,or 5 or more H-bonding interactions, and/or, e.g., 1, 2, 3, 4, or 5 vander Waals interactions with 1 or more amino acids of MASP-2 lining theS1 pocket of MASP-2, such as those amino acids selected from the groupconsisting of including ASP 627, SER 628, CYS 629, SER 633, TRP 655, GLY656, SER 657, CYS 660, GLY 667, and TYR 669.

S2 shelf: While not being limited by any theory, it is understood thatselectivity for MASP-2 inhibition over thrombin can be increased byincluding groups that interact with the S2 region of MASP-2. Forexample, M₃ moieties can provide selective MASP-2 inhibition overthrombin by the introduction of substituents on a glycine carbon ornitrogen. The S2 region of MASP-2 can accommodate both large and smallsubstituents, which can form H-bonds and van der Waals contacts withsurface lining residues (such as the peptide backbone of SER 654, thepeptide backbone and carbonyl of TRP 655 and GLY 656, and the side-chainof HIS 483), but a similar binding pose in thrombin is unfavored due tosteric interactions. Thus, it is understood that compounds havingselectivity for inhibiting MASP-2 over thrombin can be compounds thatmake interactions with the amino acids in the S-2 region of MASP-2. Forexample, the MASP-2 selective inhibitors can include compounds thatmake, e.g., 1, 2, 3, 4, or 5 or more H-bonding interactions, and/or,e.g., 1, 2, 3, 4, or 5 van der Waals interactions with 1 or more aminoacids of MASP-2 in the S2 region of MASP-2, such as those amino acidsselected from the group consisting of SER 654, TRP 655, GLY 656, and HIS483.

S3 entry indentation: While not being limited by any theory, it isunderstood that selectivity for MASP-2 inhibition over thrombin can befavored by introducing groups that interact with the S3 entry site inMASP-2, e.g., as a linker element connecting M₃ and M₄ moieties, such asplanar aromatic groups and/or groups that can form a hydrogen bondacceptor via the carbonyl group of GLY 656. In MASP-2 the S3 entry siteis composed of the first two amino acids of the 5 amino acid sequencethat includes the amino acids GLY 656, SER 657, MET 658, ASN 659 and CYS660, while in thrombin (1k22.pdb) the corresponding site is composed ofonly the first of a 4 amino acid sequence (comprising the amino acidsGLY 216, GLU 217, GLY 219 and Cys220). As a result of the correspondingshortened sequence in thrombin, the GLY 216 carbonyl group is displacedand cannot form favorable interactions with compounds that interact withthe corresponding region of MASP-2. Thus, it is understood thatcompounds having selectivity for inhibiting MASP-2 over thrombin can becompounds that make interactions with the amino acids at the S3 entrysite of MASP-2. For example, the MASP-2 selective inhibitors can includecompounds that make, e.g., 1, 2, 3, 4, or 5 or more H-bondinginteractions, and/or, e.g., 1, 2, 3, 4, or 5 van der Waals interactionswith 1 or more amino acids of MASP-2 lining at the S3 entry site ofMASP-2, such as those amino acids selected from the group consisting ofGLY 656, SER 657, MET 658, ASN 659 and CYS 660.

G. Compounds Defined by Reference to a Pharmacophore Model

The present disclosure also provides small molecules inhibitors ofMASP-2 that may be described by reference to a pharmacophore model. Ithas been found that compounds that are capable of binding to andinhibiting MASP-2, and, in particular, compounds that bind to MASP-2according to the binding rules described above can be described in termsof their structural features using a pharmacophore model.

The pharmacophore model described in Table 1 and its propertiesdisplayed in FIG. 67-75 represents averaged pharmacophore elements ofMASP-2 inhibitors as obtained by PHASE analysis after proteinpreparation and protein structure alignment with the Small-Molecule DrugDiscovery Suite 2018-4 (Schrödinger, LLC, New York, N.Y. 2018) andclustered with KMeans from sklearn (version 0.20.3; Machine Learning inPython, Pedregosa et al., JMLR 12, pp. 2825-2830, 2011).

The PHASE methodology for pharmacophore analysis has been describedgenerally in Dixon et al., J. Comput. Aided Mol. Des., 2006, 20,647-671, and Dixon et al., Chem. Biol. Drug Des., 2006, 67, 370-372. Theanalysis was performed with Prody (Bakan et al., Bioinformatics, 2011,27(11), 1575-1577; Bakan et al., Bioinformatics, 2014, 30(18),2681-2683), and the Python programing language.

Briefly, the crystal structures of small molecule inhibitors describedherein bound to human MASP-2 small molecule crystal structures wereprepared within Maestro version 2018-4 (Schrödinger, LLC). Hydrogenswere added, protonation states were adjusted, and hydrogen bondinteractions optimized. In cases where several molecules with differentconformations and/or binding modes were identified in the asymmetricunit (ASU), these were split and treated as separate protein ligandcomplexes. In addition, disordered small molecules were treated asseparate ligand conformation. The heavy atom coordinates were notmodified, i.e., through minimization.

The prepared structures were then aligned by using all backbone atomswithin 10 Å of each small molecule without residues 594-611 of SEQ IDNO:1.

Protein atoms, solvent atoms and ions are deleted to obtain an alignmentof small molecule poses only.

The program create_molSites from Schrödinger, LLC was used to converteach small molecule into separate 3-dimensional pharmacophores. Besidesthe standard feature definitions, an additional pharmacophore elementwas created to consider that positive ionizable groups can also behydrogen bond donors. In later analysis this feature was merged with thestandard hydrogen bond donor feature. The definition of positiveionizable groups (N) was extended to include groups with pKa≥6.0 (ascalculated using Epik (Schrödinger, LLC)). An alignment of pharmacophoreelements from the small molecules is obtained.

KMeans from sklearn is used to cluster the so obtained alignment of allpharmacophore elements by cartesian coordinates. After several tries thenumber of cluster centers for each pharmacophore feature was chosen tomimic experimentally observed SAR, and few pharmacophore elements weredeleted. All cluster centers represent the averaged features of theoverall pharmacophore.

Python 3.6 and Prody were used to perform the analysis.

In the PHASE method, each ligand structure is represented by a set ofpoints in 3D space, which coincide with various chemical features thatmay facilitate non-covalent binding between the ligand and its targetreceptor. These pharmacophore sites can be characterized by type,location and, if applicable, directionality. Pharmacophore elementsinclude: hydrogen bond acceptor (O), hydrogen bond donor (H),hydrophobic group (C), negative ionizable group (X), positive ionizablegroup (N), and aromatic ring (CA).

A hydrogen bond acceptor site (O) is positioned on a surface-accessibleatom that carries one or more donatable lone pairs, and a vectorattribute is assigned to each idealized hydrogen bond axis, according tothe hybridization of the acceptor atom.

A hydrogen bond donor site (H) is centered on each donatable hydrogenatom, and a single vector feature is directed along its idealizedhydrogen bond axis.

Hydrophobic groups (C) are assigned using a procedure that has beendescribed by Greene et al., J. Chem. Inf. Comput. Sci. 1994, 34, 1297.Rings, isopropyl groups, t-butyl groups, various halogenated moieties,and chains as long as four carbons are each treated as a singlehydrophobic site. Chains of five or more carbons are broken into smallerfragments containing between two and four carbons and each fragment isdesignated as a separate hydrophobic site. The location of a givenhydrophobic site is a weighted average (r_(H)) of the positions of thenon-hydrogen atoms in the associated fragment.

$r_{H} = \frac{\sum\limits_{i}{s_{i}t_{i}r_{i}}}{\sum\limits_{i}{s_{i}t_{i}}}$

Here, s_(i) is the solvent-accessible surface area of atom i, computedusing a probe radius of 1.4 Å, and t_(i) is a hydrophobicity factor thatranges between 0 and 1 (polar atoms (O, N, S) are assigned ahydrophobicity of 0, carbons and halogens at least three bonds from anypolar atom receive a value of 1; and intermediate hydrophobicities areassigned to carbons and halogens when polar atoms are within a distanceof two bonds).

Positive ionizable groups (N) and negative ionizable groups (X) aremodeled as a single point located on a formally charged atom, or at thecentroid of a group of atoms over which the ionic charge is shared. Asnoted above, in the present analysis, the definition of positiveionizable groups was extended to include positive ionizable groups witha pKa≥6.0. Thus, a positive ionizable group pharmacophore element asdescribed herein should be understood to include positive ionizablegroups with a pKa≥6.0 (as calculated using Epik (Schrödinger, LLC)).

Aromatic rings (CA) may be distinguished from other hydrophobic groups,and are designated as a separate type of pharmacophore feature,represented by a single site placed at the centroid of each aromaticring, and a two-headed vector normal to the plane of the ring isassociated with the site.

For this analysis presented herein, only the position of eachpharmacophore element was used, and vector type information was notconsidered.

The pharmacophore analysis found that compounds active as MASP-2inhibitors included combinations of one or more, for example,combinations of the elements listed in Table 1. Table 1 lists thepharmacophore elements of MASP-2 inhibitor compounds designatedaccording to element type and cartesian coordinates (x, y, z)identifying the relative position of the pharmacophore elements on anangstrom scale. The origin of the cartesian system is defined based onthe average position of all the pharmacophore elements O2, which wasdefined as (0.0, 0.0, 0.0). The cartesian coordinates given representaverage (mean) values for the coordinates of each pharmacophore element.Table 1 lists standard deviations for the values of the x, y, and zcoordinates for the ligands studied.

While not being limited by any theory, it is understood that compoundsthat are active as inhibitors of MASP-2 will include at least one or twoand preferably combinations of three or more of the pharmacophoreelements listed in Table 1. For example, the compounds that are activeas inhibitors of MASP-2 may include one or combinations of 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 of thepharmacophore elements, preferably combinations of 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13 or 14 or more of the pharmacophore elements listed inTable 1.

While not being limited by any theory, it is understood that a compoundis considered to include a pharmacophore element or combination ofpharmacophore elements as listed in Table 1 if the pharmacophore elementor combination of pharmacophore elements is present in the compound andthe compound has an accessible conformation at physiological temperature(37° C.) which can place the pharmacophore element(s) within fourstandard deviations, preferably within three standard deviations, morepreferably within two standard deviations and most preferably within onestandard deviation of the mean value for x, y and z listed in Table 1.The range defined by the mean value of each of the x, y, and zcoordinates and error allowed for (plus or minus four, three, two or onestandard deviation) can be considered to define a box within which thepharmacophore elements should be found for an active MASP-2 inhibitorcompound.

Table 2A lists the coordinates of the pharmacophore elements listed asranges of the mean (x, y, z) coordinates plus or minus one or twostandard deviations. Table 2B lists the coordinates of the pharmacophoreelements listed as ranges of the mean (x, y, z) coordinates plus orminus three or four standard deviations.

TABLE 1 Pharmacophore Elements for MASP-2 Inhibitors and theirCoordinates standard standard standard Pharmacophore Element x valuedeviation y value deviation z value deviation Type Label (average) of x(average) of y (average) of z Hydrophobic group C2 0.30 1.18 1.17 1.35−2.76 1.59 Hydrophobic group C3 −0.41 0.89 −2.85 1.66 4.64 0.12Hydrophobic group C4 4.09 1.32 5.54 0.95 −4.66 1.24 Hydrophobic group C52.64 0.22 −4.84 0.22 4.79 0.29 Hydrophobic group C6 6.01 0.75 2.84 0.54−2.56 0.34 Hydrophobic group C7 −0.85 0.35 −5.92 0.29 0.26 0.85 Aromaticring CA1 −0.61 0.50 −3.55 0.38 2.50 0.57 Aromatic ring CA2 4.00 0.483.49 0.32 −3.49 0.36 Aromatic ring CA3 −5.29 0.84 −1.15 1.48 −2.77 1.09Aromatic ring CA4 4.02 1.46 5.89 0.76 −3.90 0.21 Aromatic ring CA5 1.841.28 2.62 1.27 −5.13 0.90 Aromatic ring CA6 −1.88 1.11 2.21 0.59 −1.851.73 H bond donor H1 −8.33 0.06 −1.98 0.05 −5.56 0.06 H bond donor H2−2.25 0.35 −2.33 0.70 2.28 0.96 H bond donor H3 −0.36 0.59 −3.03 2.11−0.98 1.00 H bond donor H4 −0.28 0.75 −1.61 1.68 3.01 0.56 PositiveIonizable Group N1 0.10 0.57 −5.35 1.00 1.66 0.89 Positive IonizableGroup N2 −0.49 0.37 −0.11 0.48 −2.46 0.37 H bond acceptor O1 −2.52 0.680.57 0.72 2.02 0.57 H bond acceptor O2 0.00 0.74 0.00 0.67 0.00 0.88 Hbond acceptor O3 −6.82 2.89 −1.48 3.03 −5.36 3.59 H bond acceptor O4−1.97 0.77 −3.24 0.66 2.08 0.53

TABLE 2A Pharmacophore Elements Coordinate Ranges MASP-2 InhibitorsRange for (x, y, z) ± 1 standard deviation Range for (x, y, z) ± 2standard deviations Label x y z x y z C2   0.30 ± 1.18   1.17 ± 1.35−2.76 ± 1.59   0.30 ± 2.37   1.17 ± 2.69 −2.76 ± 3.18 C3 −0.41 ± 0.89−2.85 ± 1.66   4.64 ± 0.12 −0.41 ± 1.78 −2.85 ± 3.32   4.64 ± 0.23 C4  4.09 ± 1.32   5.54 ± 0.95 −4.66 ± 1.24   4.09 ± 2.63   5.54 ± 1.89−4.66 ± 2.49 C5   2.64 ± 0.22 −4.84 ± 0.22   4.79 ± 0.29   2.64 ± 0.43−4.84 ± 0.45   4.79 ± 0.59 C6   6.01 ± 0.75   2.84 ± 0.54 −2.56 ± 0.34  6.01 ± 1.50   2.84 ± 1.07 −2.56 ± 0.67 C7 −0.85 ± 0.35 −5.92 ± 0.29  0.26 ± 0.85 −0.85 ± 0.70 −5.92 ± 0.58   0.26 ± 1.71 CA1 −0.61 ± 0.50−3.55 ± 0.38   2.50 ± 0.57 −0.61 ± 1.00 −3.55 ± 0.76   2.50 ± 1.13 CA2  4.00 ± 0.48   3.49 ± 0.32 −3.49 ± 0.36   4.00 ± 0.96   3.49 ± 0.65−3.49 ± 0.72 CA3 −5.29 ± 0.84 −1.15 ± 1.48 −2.77 ± 1.09 −5.29 ± 1.68−1.15 ± 2.96 −2.77 ± 2.17 CA4   4.02 ± 1.46   5.89 ± 0.76 −3.90 ± 0.21  4.02 ± 2.92   5.89 ± 1.52 −3.90 ± 0.41 CA5   1.84 ± 1.28   2.62 ± 1.27−5.13 ± 0.90   1.84 ± 2.55   2.62 ± 2.53 −5.13 ± 1.80 CA6 −1.88 ± 1.11  2.21 ± 0.59 −1.85 ± 1.73 −1.88 ± 2.23   2.21 ± 1.18 −1.85 ± 3.46 H1−8.33 ± 0.06 −1.98 ± 0.05 −5.56 ± 0.06 −8.33 ± 0.12 −1.98 ± 0.11 −5.56 ±0.11 H2 −2.25 ± 0.35 −2.33 ± 0.70   2.28 ± 0.96 −2.25 ± 0.69 −2.33 ±1.41   2.28 ± 1.93 H3 −0.36 ± 0.59 −3.03 ± 2.11 −0.98 ± 1.00 −0.36 ±1.17 −3.03 ± 4.21 −0.98 ± 2.01 H4 −0.28 ± 0.75 −1.61 ± 1.68   3.01 ±0.56 −0.28 ± 1.49 −1.61 ± 3.35   3.01 ± 1.12 N1   0.10 ± 0.57 −5.35 ±1.00   1.66 ± 0.89   0.10 ± 1.13 −5.35 ± 2.00   1.66 ± 1.78 N2 −0.49 ±0.37 −0.11 ± 0.48 −2.46 ± 0.37 −0.49 ± 0.74 −0.11 ± 0.96 −2.46 ± 0.75 O1−2.52 ± 0.68   0.57 ± 0.72   2.02 ± 0.57 −2.52 ± 1.35   0.57 ± 1.44  2.02 ± 1.13 O2   0.00 ± 0.74   0.00 ± 0.67   0.00 ± 0.88   0.00 ± 1.49  0.00 ± 1.33   0.00 ± 1.77 O3 −6.82 ± 2.89 −1.48 ± 3.03 −5.36 ± 3.59−6.82 ± 5.78 −1.48 ± 6.06 −5.36 ± 7.19 O4 −1.97 ± 0.77 −3.24 ± 0.66  2.08 ± 0.53 −1.97 ± 1.54 −3.24 ± 1.33   2.08 ± 1.06

TABLE 2B Pharmacophore Elements Coordinate Ranges MASP-2 InhibitorsRange for (x, y, z) ± 3 standard deviations Range for (x, y, z) ± 4standard deviations Label x y z x y z C2   0.30 ± 3.55   1.17 ± 4.04−2.76 ± 4.77   0.30 ± 4.74   1.17 ± 5.38 −2.76 ± 6.36 C3 −0.41 ± 2.67−2.85 ± 4.98   4.64 ± 0.35 −0.41 ± 3.56 −2.85 ± 6.64   4.64 ± 0.47 C4  4.09 ± 3.95   5.54 ± 2.84 −4.66 ± 3.73   4.09 ± 5.26   5.54 ± 3.79−4.66 ± 4.97 C5   2.64 ± 0.65 −4.84 ± 0.67   4.79 ± 0.88   2.64 ± 0.86−4.84 ± 0.89   4.79 ± 1.17 C6   6.01 ± 2.25   2.84 ± 1.61 −2.56 ± 1.01  6.01 ± 3.00   2.84 ± 2.14 −2.56 ± 1.34 C7 −0.85 ± 1.04 −5.92 ± 0.87  0.26 ± 2.56 −0.85 ± 1.39 −5.92 ± 1.16   0.26 ± 3.41 CA1 −0.61 ± 1.49−3.55 ± 1.15   2.50 ± 1.70 −0.61 ± 1.99 −3.55 ± 1.53   2.5 ± 2.26 CA2  4.00 ± 1.43   3.49 ± 0.97 −3.49 ± 1.07   4.00 ± 1.91   3.49 ± 1.29−3.49 ± 1.43 CA3 −5.29 ± 2.52 −1.15 ± 4.44 −2.77 ± 3.26 −5.29 ± 3.36−1.15 ± 5.92 −2.77 ± 4.35 CA4   4.02 ± 4.37   5.89 ± 2.29 −3.90 ± 0.62  4.02 ± 5.83   5.89 ± 3.05  −3.9 ± 0.83 CA5   1.84 ± 3.83   2.62 ± 3.80−5.13 ± 2.70   1.84 ± 5.11   2.62 ± 5.06 −5.13 ± 3.60 CA6 −1.88 ± 3.34  2.21 ± 1.76 −1.85 ± 5.19 −1.88 ± 4.46   2.21 ± 2.35 −1.85 ± 6.92 H1−8.33 ± 0.18 −1.98 ± 0.16 −5.56 ± 0.17 −8.33 ± 0.24 −1.98 ± 0.22 −5.56 ±0.23 H2 −2.25 ± 1.04 −2.33 ± 2.11   2.28 ± 2.89 −2.25 ± 1.38 −2.33 ±2.82   2.28 ± 3.86 H3 −0.36 ± 1.76 −3.03 ± 6.32 −0.98 ± 3.01 −0.36 ±2.34 −3.03 ± 8.43 −0.98 ± 4.01 H4 −0.28 ± 2.24 −1.61 ± 5.03   3.01 ±1.68 −0.28 ± 2.99 −1.61 ± 6.71   3.01 ± 2.24 N1   0.10 ± 1.70 −5.35 ±3.00   1.66 ± 2.68   0.10 ± 2.26 −5.35 ± 4.00   1.66 ± 3.57 N2 −0.49 ±1.11 −0.11 ± 1.45 −2.46 ± 1.12 −0.49 ± 1.48 −0.11 ± 1.93 −2.46 ± 1.50 O1−2.52 ± 2.03   0.57 ± 2.16   2.02 ± 1.70 −2.52 ± 2.70   0.57 ± 2.88  2.02 ± 2.27 O2   0.00 ± 2.23   0.00 ± 2.00   0.00 ± 2.65   0.00 ± 2.98  0.00 ± 2.66   0.00 ± 3.54 O3 −6.82 ± 8.67 −1.48 ± 9.09  −5.36 ± 10.78 −6.82 ± 11.56  −1.48 ± 12.12  −5.36 ± 14.37 O4 −1.97 ± 2.32 −3.24 ±1.99   2.08 ± 1.59 −1.97 ± 3.09 −3.24 ± 2.65   2.08 ± 2.12

The present disclosure provides a compound for use in the treatment ofMASP-2-associated diseases or disorders, wherein the compound comprisesa combination of pharmacophore elements comprising:

(a) an S1 pharmacophore group comprising CA1 and N1 pharmacophoreelements or CA1 and C5 pharmacophore elements; and/or

(b) an S2 pharmacophore group comprising H4 and O2 pharmacophoreelements; and/or

(c) an S3 pharmacophore group comprising a C2 pharmacophore element andan N2 or H3 pharmacophore element;

wherein:

C2 and C5 are hydrophobic groups;

CA1 is an aromatic ring;

H3 and H4 are hydrogen bond donors;

N1 and N2 are positive ionizable groups; and

O2 is a hydrogen bond acceptor;

wherein C2, C5, CA1, H3, H4, N1, N2, and O2 have coordinates in theranges given in Table 3, 4, or 5 below.

In some embodiments, the compound comprises a combination ofpharmacophore elements comprising:

(a) an S1 pharmacophore group comprising CA1 and N1 pharmacophoreelements or CA1 and C5 pharmacophore elements; and

(b) an S2 pharmacophore group comprising H4 and O2 pharmacophoreelements; and

(c) an S3 pharmacophore group comprising a C2 pharmacophore element andan N2 or H3 pharmacophore element.

wherein C2, C5, CA1, H3, H4, N1, N2, and O2 have coordinates in theranges given in Table 3, 4, or 5 below.

In some embodiments, C2, C5, CA1, H3, H4, N1, N2, and O2 havecoordinates in the ranges given in Table 3 below:

TABLE 3 Pharmacophore element x coordinate y coordinate z coordinates C2  0.30 ± 3.55   1.17 ± 4.04 −2.76 ± 4.77 C5   2.64 ± 0.65 −4.84 ± 0.67  4.79 ± 0.88 CA1 −0.61 ± 1.49 −3.55 ± 1.15   2.50 ± 1.70 H3 −0.36 ±1.76 −3.03 ± 6.32 −0.98 ± 3.01 H4 −0.28 ± 2.24 −1.61 ± 5.03   3.01 ±1.68 N1   0.10 ± 1.70 −5.35 ± 3.00   1.66 ± 2.68 N2 −0.49 ± 1.11 −0.11 ±1.45 −2.46 ± 1.12 O2   0.00 ± 2.23   0.00 ± 2.00   0.00 ± 2.65

In some embodiments, C2, C5, CA1, H3, H4, N1, N2, and O2 havecoordinates in the ranges given in Table 4 below:

TABLE 4 Pharmacophore element x coordinate y coordinate z coordinates C2  0.30 ± 2.37   1.17 ± 2.69 −2.76 ± 3.18 C5   2.64 ± 0.43 −4.84 ± 0.45  4.79 ± 0.59 CA1 −0.61 ± 1.00 −3.55 ± 0.76   2.50 ± 1.13 H3 −0.36 ±1.17 −3.03 ± 4.21 −0.98 ± 2.01 H4 −0.28 ± 1.49 −1.61 ± 3.35   3.01 ±1.12 N1   0.10 ± 1.13 −5.35 ± 2.00   1.66 ± 1.78 N2 −0.49 ± 0.74 −0.11 ±0.96 −2.46 ± 0.75 O2   0.00 ± 1.49   0.00 ± 1.33   0.00 ± 1.77

In some embodiments, C2, C5, CA1, H3, H4, N1, N2, and O2 havecoordinates in the ranges given in Table 5 below:

TABLE 5 Pharmacophore element x coordinate y coordinate z coordinates C2  0.30 ± 1.18   1.17 ± 1.35 −2.76 ± 1.59 C5   2.64 ± 0.22 −4.84 ± 0.22  4.79 ± 0.29 CA1 −0.61 ± 0.5  −3.55 ± 0.38    2.5 ± 0.57 H3 −0.36 ±0.59 −3.03 ± 2.11 −0.98 ± 1.00 H4 −0.28 ± 0.75 −1.61 ± 1.68   3.01 ±0.56 N1   0.10 ± 0.57 −5.35 ± 1.00   1.66 ± 0.89 N2 −0.49 ± 0.37 −0.11 ±0.48 −2.46 ± 0.37 O2   0.00 ± 0.74   0.00 ± 0.67   0.00 ± 0.88

In some embodiments, the S1 pharmacophore group comprises CA1 and N1pharmacophore elements.

In some embodiments, the S1 pharmacophore group further comprises a C3pharmacophore element, wherein C3 is a hydrophobic group and hascoordinates in the ranges given in Table 6 below.

TABLE 6 Pharmacophore element x coordinate y coordinate z coordinates C3−0.41 ± 2.67 −2.85 ± 4.98 4.64 ± 0.35

In some embodiments, C3 has coordinates in the ranges given in Table 7below.

TABLE 7 Pharmacophore element x coordinate y coordinate z coordinates C3−0.41 ± 1.78 −2.85 ± 3.32 4.64 ± 0.23

In some embodiments, C3 has coordinates in the ranges given in Table 8below.

TABLE 8 Pharmacophore element x coordinate y coordinate z coordinates C3−0.41 ± 0.89 −2.85 ± 1.66 4.64 ± 0.12

In some embodiments, the S1 pharmacophore group comprises CA1 and C5pharmacophore elements.

In some embodiments, the S1 pharmacophore group further comprises 1, 2,or 3 pharmacophore elements selected from the group consisting of C7, H2and O4, wherein:

C7 is a hydrophobic group;

H2 is a hydrogen bond donor; and

O4 is a hydrogen bond acceptor; and

wherein C7, H2 and O4 have the coordinates in the ranges given in Table9 below:

TABLE 9 Pharmacophore element x coordinate y coordinate z coordinates C7−0.85 ± 1.04 −5.92 ± 0.87 0.26 ± 2.56 H2 −2.25 ± 1.04 −2.33 ± 2.11 2.28± 2.89 O4 −1.97 ± 2.32 −3.24 ± 1.99 2.08 ± 1.59

In some embodiments, C7, H2 and O4 have coordinates in the ranges givenin Table 10 below:

TABLE 10 Pharmacophore element x coordinate y coordinate z coordinatesC7 −0.85 ± 0.70 −5.92 ± 0.58 0.26 ± 1.71 H2 −2.25 ± 0.69 −2.33 ± 1.412.28 ± 1.93 O4 −1.97 ± 1.54 −3.24 ± 1.33 2.08 ± 1.06

In some embodiments, C7, H2 and O4 have coordinates in the ranges givenin Table 11 below:

TABLE 11 Pharmacophore element x coordinate y coordinate z coordinatesC7 −0.85 ± 0.35 −5.92 ± 0.29 0.26 ± 0.85 H2 −2.25 ± 0.35 −2.33 ± 0.7 2.28 ± 0.96 O4 −1.97 ± 0.77 −3.24 ± 0.66 2.08 ± 0.53

In some embodiments, the S1 pharmacophore group comprises a C7pharmacophore element.

In some embodiments, the S1 pharmacophore group comprises an H2pharmacophore element.

In some embodiments, the S1 pharmacophore group comprises an O4pharmacophore element.

In some embodiments, the S2 pharmacophore group further comprises 1 or 2pharmacophore elements selected from the group consisting of CA6 and O1,wherein:

CA6 is an aromatic ring;

O1 is a hydrogen bond acceptor;

wherein CA6 and O1 have coordinates in the ranges given in Table 12below:

TABLE 12 Pharmacophore element x coordinate y coordinate z coordinatesCA6 −1.88 ± 3.34 2.21 ± 1.76 −1.85 ± 5.19 O1 −2.52 ± 2.03 0.57 ± 2.16  2.02 ± 1.70

In some embodiments, CA6 and O1 have coordinates in the ranges given inTable 13 below:

TABLE 13 Pharmacophore element x coordinate y coordinate z coordinatesCA6 −1.88 ± 2.23 2.21 ± 1.18 −1.85 ± 3.46 O1 −2.52 ± 1.35 0.57 ± 1.44  2.02 ± 1.13

In some embodiments, CA6 and O1 have coordinates in the ranges given inTable 14 below:

TABLE 14 Pharmacophore element x coordinate y coordinate z coordinatesCA6 −1.88 ± 1.11 2.21 ± 0.59 −1.85 ± 1.73 O1 −2.52 ± 0.68 0.57 ± 0.72  2.02 ± 0.57

In some embodiments, the S1 pharmacophore group comprises a CA6pharmacophore element.

In some embodiments, the S1 pharmacophore group comprises an O1pharmacophore element.

In some embodiments, the S3 pharmacophore group comprises C2 and N2pharmacophore elements.

In some embodiments, the S3 pharmacophore group further comprises an H3pharmacophore element.

In some embodiments, the compound further comprises an S4 pharmacophoregroup; wherein the S4 pharmacophore group comprises a C4, CA2, CA4 orCA5 pharmacophore element; wherein

C4 is a hydrophobic group; and

CA2, CA4, and CA5 are aromatic rings; and

wherein C4, CA2, CA4, and CA5 have coordinates in the ranges given inTable 15 below:

TABLE 15 Pharmacophore element x coordinate y coordinate z coordinatesC4 4.09 ± 3.95 5.54 ± 2.84 −4.66 ± 3.73 CA2 4.00 ± 1.43 3.49 ± 0.97−3.49 ± 1.07 CA4 4.02 ± 4.37 5.89 ± 2.29 −3.90 ± 0.62 CA5 1.84 ± 3.832.62 ± 3.80 −5.13 ± 2.70

In some embodiments, C4, CA2, CA4, and CA5 have coordinates in theranges given in Table 16 below:

TABLE 16 Pharmacophore element x coordinate y coordinate z coordinatesC4 4.09 ± 2.63 5.54 ± 1.89 −4.66 ± 2.49 CA2 4.00 ± 0.96 3.49 ± 0.65−3.49 ± 0.72 CA4 4.02 ± 2.92 5.89 ± 1.52 −3.90 ± 0.41 CA5 1.84 ± 2.552.62 ± 2.53 −5.13 ± 1.80

In some embodiments, C4, CA2, CA4, and CA5 have coordinates in theranges given in Table 17 below:

TABLE 17 Pharmacophore element x coordinate y coordinate z coordinatesC4 4.09 ± 1.32 5.54 ± 0.95 −4.66 ± 1.24 CA2 4.00 ± 0.48 3.49 ± 0.32−3.49 ± 0.36 CA4 4.02 ± 1.46 5.89 ± 0.76 −3.90 ± 0.21 CA5 1.84 ± 1.282.62 ± 1.27 −5.13 ± 0.90

In some embodiments, the S4 pharmacophore group comprises C4.

In some embodiments, the S4 pharmacophore group comprises CA2.

In some embodiments, the S4 pharmacophore group comprises CA4.

In some embodiments, the S4 pharmacophore group comprises CA5.

In some embodiments, the S4 pharmacophore group further comprises 1, 2,3, or 4 additional pharmacophore elements selected from the groupconsisting of C6, C7, CA4 and CA5, wherein:

C6 and C7 are hydrophobic groups; and

CA4 and CA5 are aromatic rings; and

wherein C6, C7, CA4, and CA5 have coordinates in the ranges given inTable 18 below:

TABLE 18 Pharmacophore element x coordinate y coordinate z coordinatesC6   6.01 ± 2.25   2.84 ± 1.61 −2.56 ± 1.01 C7 −0.85 ± 1.04 −5.92 ± 0.87  0.26 ± 2.56 CA4   4.02 ± 4.37   5.89 ± 2.29 −3.90 ± 0.62 CA5   1.84 ±3.83   2.62 ± 3.80 −5.13 ± 2.70

In some embodiments, C6, C7, CA4, and CA5 have coordinates in the rangesgiven in Table 19 below:

TABLE 19 Pharmacophore element x coordinate y coordinate z coordinatesC6   6.01 ± 1.50   2.84 ± 1.07 −2.56 ± 0.67 C7 −0.85 ± 0.70 −5.92 ± 0.58  0.26 ± 1.71 CA4   4.02 ± 2.92   5.89 ± 1.52 −3.90 ± 0.41 CA5   1.84 ±2.55   2.62 ± 2.53 −5.13 ± 1.80

In some embodiments, C6, C7, CA4, and CA5 have coordinates in the rangesgiven in Table 20 below:

TABLE 20 Pharmacophore element x coordinate y coordinate z coordinatesC6   6.01 ± 0.75   2.84 ± 0.54 −2.56 ± 0.34 C7 −0.85 ± 0.35 −5.92 ± 0.29  0.26 ± 0.85 CA4   4.02 ± 1.46   5.89 ± 0.76 −3.90 ± 0.21 CA5   1.84 ±1.28   2.62 ± 1.27 −5.13 ± 0.90

In some embodiments, the S4 pharmacophore group comprises a C6pharmacophore element.

In some embodiments, the S4 pharmacophore group comprises a C7pharmacophore element.

In some embodiments, the S4 pharmacophore group comprises a CA4pharmacophore element.

In some embodiments, the S4 pharmacophore group comprises a CA5pharmacophore element.

In some embodiments, the compound further comprises an RM pharmacophoregroup; wherein the RM pharmacophore group comprises a CA3 pharmacophoreelement, wherein CA3 is an aromatic ring that has coordinates in theranges given in Table 21 below:

TABLE 21 Pharmacophore element x coordinate y coordinate z coordinatesCA3 −5.29 ± 2.52 −1.15 ± 4.44 −2.77 ± 3.26

In some embodiments, CA3 has coordinates in the ranges given in Table 22below:

TABLE 22 Pharmacophore element x coordinate y coordinate z coordinatesCA3 −5.29 ± 1.68 −1.15 ± 2.96 −2.77 ± 2.17

In some embodiments, CA3 has coordinates in the ranges given in Table 23below: Table 23.

TABLE 23 Pharmacophore element x coordinate y coordinate z coordinatesCA3 −5.29 ± 0.84 −1.15 ± 1.48 −2.77 ± 1.09

In some embodiments, the RM pharmacophore group further comprises 1 or 2additional pharmacophore elements selected from the group consisting ofH1 and O3, wherein:

H1 is a hydrogen bond donor; and

O3 is a hydrogen bond acceptor; and

wherein H1 and O3 have coordinates in the ranges given in Table 24below:

TABLE 24 Pharmacophore element x coordinate y coordinate z coordinatesH1 −8.33 ± 0.18 −1.98 ± 0.16 −5.56 ± 0.17  O3 −6.82 ± 8.67 −1.48 ± 9.09−5.36 ± 10.78

In some embodiments, H1 and O3 have coordinates in the ranges given inTable 25 below:

TABLE 25 Pharmacophore element x coordinate y coordinate z coordinatesH1 −8.33 ± 0.12 −1.98 ± 0.11 −5.56 ± 0.11 O3 −6.82 ± 5.78 −1.48 ± 6.06−5.36 ± 7.19

In some embodiments, H1 and O3 have coordinates in the ranges given inTable 26 below:

TABLE 26 Pharmacophore element x coordinate y coordinate z coordinatesH1 −8.33 ± 0.06 −1.98 ± 0.05 −5.56 ± 0.06 O3 −6.82 ± 2.89 −1.48 ± 3.03−5.36 ± 3.59

In some embodiments, the RM pharmacophore group comprises H1.

In some embodiments, the RM pharmacophore group comprises O3.

FIG. 66 shows a schematic representation of the MASP+2 bindingsub-pockets. While not being limited by any theory, it is understoodthat certain pharmacophore groups and elements are associated withbinding to certain regions of the MASP-2 protein. For clarity reasonsonly, some of the sub-pockets are shown and referred to in thediscussion and additional figures below.

Certain combinations of the pharmacophore elements listed in Table 1were found to be favorable and associated with more potent activity. Inparticular, in some embodiments, effective MASP-2 inhibitors can includeS1, S2 and/or S3 pharmacophore groups. In some embodiments, effectiveMASP-2 inhibitors can include S1, S2, S3 and/or S4 pharmacophore groups.

In some embodiments, the S1 pharmacophore group can be selected from thepharmacophore groups S1a, S1b and S1c, wherein:

the S1a pharmacophore group includes the pharmacophore elements CA1 andN1;

the S1b pharmacophore group includes the pharmacophore elements CA1, N1and C3; and

the S1c pharmacophore group includes the pharmacophore elements CA1 andC5 elements, and can also optionally include 1, 2, 3 or 4 of thepharmacophore elements C5, C7, H2 and/or O4.

The S2 pharmacophore group includes the pharmacophore elements H4 andO2, and can optionally also include the pharmacophore elements O1 and/orCA6.

In some embodiments, the S3 pharmacophore group can be selected from thepharmacophore groups S3a and S3b, wherein:

the S3a pharmacophore group includes the pharmacophore elements C2 andN2, and can optionally also include the pharmacophore element H3; and

the S3b pharmacophore group includes the pharmacophore elements C3 andH3.

The compounds can also include an S4 pharmacophore group.

In some embodiments, the S4 pharmacophore group can be selected from thepharmacophore groups S4a, S4b, S4c, S4d, S4e and S4f, wherein:

the S4a pharmacophore group includes the pharmacophore element CA2, andcan optionally also include 1, 2, 3, or 4 of the pharmacophore elementsC6, C7, CA4 and/or CA5;

the S4b pharmacophore group includes the pharmacophore element CA2;

the S4c pharmacophore group includes the pharmacophore elements CA2 andCA4;

the S4d pharmacophore group includes the pharmacophore elements CA2 andC6;

the S4e pharmacophore group includes the pharmacophore element CA5; and

the S4e pharmacophore group includes the pharmacophore element C4.

The compounds can also include an RM pharmacophore group, which includesthe pharmacophore element CA3. The RM pharmacophore group can alsooptionally include 1 or 2 pharmacophore elements selected from H1 and/orH3.

Preferred are combinations where S1, S2, S3 and S4 pharmacophore groupsare present. An RM pharmacophore group can also optionally be present.

Table 27 provides a listing of pharmacophore group elements andcombinations. Optional elements are shown in parentheses.

TABLE 27 Listing of Pharmacophore Group Elements and CombinationsPharmacophore groups Pharmacophore elements S1a CA1, N1 S1b CA1, N1, C3S1c CA1, C5, (C7), (O4), (H2) S2 H4, (O1), O2, (CA6) S3a N2, (H3), C2S3b H3, C2 S4a CA2, (CA4), (CA5), (C6), (C7) S4b CA2 S4c CA2, CA4 S4dCA2, C6 S4e CA5 S4f C4 RM CA3, (O3), (H1)

Elements in parentheses may be matched.

Distances between said pharmacophore elements and the closest atom ofeach ligand in its crystallized conformation are summarized in Table A4(Appendix), distances and bond and torsion angles separating atomsmatched by said pharmacophore elements are summarized in Tables A5-A7(Appendix) and defined in FIGS. 67-75 , and distances betweenpharmacophore elements and the nearest binding site residue (Table A8).

Table A4 describes the distances between individual averagedpharmacophore elements and a small molecule for a conformation of thesmall molecule as it binds into the binding site of hMASP-2. Theligand-protein complexes were experimentally determined by X-raycrystallography. The statistical values used for description in the textare summarizing all values for a specific distance. A missing valueindicates that the averaged pharmacophore element is not present in themolecule.

Table A5 describes the distances between specific atoms in a molecule asit binds into the binding site of hMASP-2 matched by selectpharmacophore elements The ligand-protein complexes were experimentallydetermined by X-ray crystallography. The statistical values used fordescription in the text are summarizing all values for each distance. Amissing value indicates that either one or two pharmacophore elementsare not present in the molecule.

Table A6 describes the angles between specific atoms in a molecule as itbinds into the binding site of hMASP-2 matched by select pharmacophoreelements. The ligand-protein complexes were experimentally determined byX-ray crystallography. The statistical values used for description inthe text are summarizing all values for each angle. A missing valueindicates that either one, two or three pharmacophore elements are notpresent in the molecule.

Table A7 describes the torsion angles between specific atoms in amolecule as it binds into the binding site of hMASP-2 matched by selectpharmacophore elements. The ligand-protein complexes were experimentallydetermined by X-ray crystallography. The statistical values used fordescription in the text are summarizing all values for each torsionangle. A missing value indicates that either one, two, three or fourpharmacophore elements are not present in the molecule.

Table A8 describes the shortest distances between each pharmacophoreelement and binding site residues of all hMASP-2 crystal structures.Starting from aligned ligand-protein complexes the small molecule inevery structure was replaced by the averaged pharmacophore model. Eachpharmacophore element can interact with several binding site residues.Furthermore, different atoms of a residue can form shortest distanceswith a pharmacophore element. The summary statistics of all distancesbetween a pharmacophore element and a residue form the basis for thedescription in the text.

The center of a pharmacophore is defined as S2 region (FIGS. 67 and 68 )(Table 27) including hydrogen bond donating group H4, hydrogen bondaccepting group O1, and hydrogen bond accepting group O2, which arehighly conserved among all compounds. An additional aromatic ring (CA6)can be matched. Potent MASP-2 inhibitor compounds match one of 4 ofthese pharmacophore elements. The distance d(H4,O1) between H4 and O1 isan average of 3.984 Å with a standard deviation of 1.071 Å, a minimum of2.084 Å, and a maximum of 6.969. Between HA and O2 the distance d(H4,O2)is an average of 3.975 Å with a standard deviation of 1.125 Å, a minimumof 2.420 Å, and a maximum of 8.835 Å. The distance d(O1,O2) between O1and O2 is an average of 3.585 Å with a standard deviation of 1.034 Å, aminimum of 2.286 Å, and a maximum of 9.569 Å. The bond angle (O1,O2,H4)as defined by O1, O2 and H4 between O1, O2 and H4 is an average of125.220 with a standard deviation of 16.57°, a minimum of 61.95°, and amaximum of 156.25°. The average distance d(CA6,O1) between CA6 and O1 is5.186 Å with a standard deviation of 1.781 Å, a minimum value of 2.732Å, and a maximum value of 7.041 Å. The average distance d(CA6,O2)between CA6 and O2 is 3.797 Å with a standard deviation of 2.477 Å, aminimum value of 1.127 Å and a maximum value of 8.449 Å. The averagebond angle ∠(O1,CA6,O2) between O1, CA6 and O2 is 106.010 with astandard deviation of 33.54°, a minimum value of 75.74° and a maximumvalue of 159.18°. The average torsion angle ∠(CA6,O1,H4,O2) as definedby CA6, O1, H4 and O2 is 17.400 with a standard deviation of 29.14°, aminimum value of −19.90° and a maximum value of 55.30°.

The pharmacophore elements in the S1 region as defined in FIGS. 67 and68 and Table 27 represent a collection of pharmacophore subsets that arepreferred for effective MASP-2 inhibition. Subsets have in common anaromatic ring CA1 which forms with O1 and O2 a bond angle ∠(CA1, O1, O2)of an average of 109.450 with a standard deviation of 12.06°, a minimumvalue of 72.650 and a maximum value of 151.69°. The average torsionangle ∠(CA1,O2,H4,O1) as defined by CA1, O2, H4 and O1 is −76.06° with astandard deviation of 50.45°, a minimum value of −175.49° and a maximumvalue of 150.81°. The average distance d(CA1, O1) between CA1 and O1 is4.703 Å and the standard deviation is 0.647 Å, the minimum value is3.345 Å and the maximum value is 7.586 Å. The average distance d(CA1,O2)between CA1 and O2 4.524 Å and the standard deviation is 0.948 Å, with aminimum value of 3.506 Å and a maximum value of 9.417 Å.

For the S1a pharmacophore group in Table 27 a positively charged groupN1 is preferred for the compounds to be efficient MASP-2 inhibitors. Theaverage distance d(CA1, N1) between CA1 and N1 is 3.463 Å and a standarddeviation of 0.426 Å, with a minimum value of 1.849 Å and a maximumvalue of 3.658 Å. The average bond angle ∠(N1,CA1,O1) between N1, CA1and O1 is 164.290 with a standard deviation of 5.24°, a minimum value of153.110 and a maximum value of 176.16°. The average torsion angle∠(N1,CA1,O2,H4) as defined by N1, CA1, O2 and H4 is −92.19° with astandard deviation of 67.16°, a minimum value of −159.59° and a maximumvalue of 106.51°.

Pharmacophore group S1b in Table 27 represents an extension ofpharmacophore group S1a with an additional hydrophobic group C3. Theaverage bond distance d(C3, CA1) between C3 and CA1 is 2.858 Å with astandard deviation of 0.010 Å, a minimum value of 2.842 Å and a maximumvalue of 2.882 Å. The average bond angle ∠(C3,CA1,O1) between C3, CA1and O1 is 149.91 degree with a standard deviation of 0.51°, a minimumvalue of 148.890 and a maximum value of 151.05°. The average torsionangle ∠(C3,CA1,O1,H4) as defined by C3, CA1, O1 and H4 is 28.540 with astandard deviation of 9.82°, a minimum value of 21.760 and a maximumvalue of 66.00°. The average distance d(CA1, N1) between CA1 and N1 is1.374 Å and a standard deviation of 0.014, a minimum of 1.336, andmaximum value of 1.392 Å. The average bond angle ∠(N1,CA1,O1) betweenN1, CA1 and O1 is 173.400 with a standard deviation of 2.20°, a minimumof 161.820 and maximum of 175.41°. The average torsion angle∠(N1,CA1,O1,H4) as defined by N1, CA1, O1 and H4 is 2.570 with astandard deviation of 29.67°, a minimum value of −107.13° and a maximumvalue of 58.16°.

The pharmacophore group S1c comprises the pharmacophore elementsaromatic ring CA1 and a hydrophobic group C5, an optional hydrogen bondacceptor O4, or hydrophobic group C7 or an optional hydrogen bonddonating group H2. The average distance d(CA1,O4) between CA2 and O4 is2.592 Å with a standard deviation of 0.367 Å, a minimum of 1.737 Å andmaximum value of 2.836 Å. The average bond angle ∠(O1,CA1,O4) betweenO1, CA1 and O4 is 64.900 with a standard deviation of 5.55°, a minimumvalue of 51.330 and a maximum value of 73.28°. The average torsion angle∠(O4,CA1,O1,H4) as defined by O4, CA1, O1 and H4 is −51.12° with astandard deviation of 146.72°, a minimum value of −176.00° and a maximumvalue of 175.38°. The average distance d(CA1, C5) between CA1 and C5 is3.173 Å with a standard deviation of 0.128 Å, a minimum value of 3.084 Åand a maximum value 3.547 Å. The average bond angle ∠(C5,CA1,O1) betweenC5, CA1 and O1 is an average of 159.21° with a standard deviation of4.12°, a minimum value of 150.20° and a maximum value of 164.79°. Theaverage torsion angle ∠(C5,CA1,O1,H4) as defined by C5, CA1, O1 and H4is −2.73° with a standard deviation of 39.57°, a minimum value of−110.81° and a maximum value of 38.04°. The average distance d(CA1, C7)between CA1 and C7 is 2.992 Å with a standard deviation of 0.067 Å, aminimum value of 2.903 Å, and a maximum value of 3.065 Å. The averagebond angle ∠(C7,CA1,O1) between C7, CA1 and O1 is 132.370 with astandard deviation of 8.18°, a minimum value of 121.010 and a maximumvalue of 139.92°. The average torsion angle ∠(C7,CA1,O1,H4) as definedby C7, CA1, O1 and H4 is −157.34° with a standard deviation of 4.95°, aminimum value of −161.01° and a maximum value of −150.35°. The averagedistance d(O4,H2) between O4 and H2 is 0.973 Å with a standard deviationof 0.007 Å, a minimum value of 0.962, and a maximum value of 0.983. Theaverage bond angle ∠(CA1,O4,H2) between CA1, O4 and H2 is 126.980 with astandard deviation of 2.30°, a minimum value of 122.200 and a maximumvalue of 131.81°. The average torsion angle ∠(H2,O4,CA1,O1) as definedby H2, O4, CA1 and O1 is 29.820 with a standard deviation of 60.96°, aminimum value of −12.92° and a maximum value of 174.89°. The S3 regionas defined in Table 27 and FIGS. 66 and 72 includes a protonatable N2and or a hydrogen bond donor H3 and a hydrophobic group C2. In thecollection of pharmacophore elements S3a,b the hydrogen bond donatinggroup H3 and/or the positive ionizable group N2 (Table 27) are preferredto provide potent inhibitors of human MASP-2. The average distance d(O2,H3) between O2 and H3 is 3.993 Å with a standard deviation of 1.422 Å, aminimum value of 1.266 Å and a maximum value of 8.995 Å. The averagebond angle ∠(O1,O2,H3) is 141.41°, with a standard deviation of 17.50°,a minimum value of 25.95°, and maximum value of 170.92°. The averagetorsion angle ∠(H4,O1,O2,H3) as defined by H4, O1, O2 and H3 is 17.91°with a standard deviation of 88.16°, a minimum value of −176.95° and amaximum value of 162.81°. The distance d(O2,N2) between O2 and N2 is2.830 Å with a standard deviation of 0.295 Å, a minimum value of 2.404 Åand a maximum value of 4.424 Å. The bond angle ∠(O1,O2,N2) is 139.320with a standard deviation of 16.79°, a minimum value of 44.760 and amaximum value of 175.07°. The average torsion angle ∠(H4,O1,O2,N2) asdefined by H4, O1, O2 and N2 is 47940 with a standard deviation of124.93°, a minimum value of −178.39° and a maximum value of 177.59°. Theaverage distance d(N2,C2) between N2 and C2 is 2.220 Å with a standarddeviation of 1.638 Å, a minimum value of 1.321 Å and a maximum value of8.529 Å. The average bond angle ∠(O2,N2,C2) between O2, N2 and C2 is130.190 with a standard deviation of 11.79°, a minimum value of 100.680and a maximum value of 168.69°. The average torsion angle ∠(O1,O2,N2,C2)as defined by O1, O2, N2 and C2 is 99.050 with a standard deviation of59.50°, a minimum value of −139.940 and maximum value of 151.54°. The S4region contains a cluster of hydrophobic groups and aromatic rings,which can be matched individually or in combination (see Table 27 andFIGS. 72-74 for details). The average distance d(N2,C4) between N2 andC4 is 7.669 Å with a standard deviation of 0.619 Å, a minimum value of6.056 Å and a maximum value of 8.240 Å. The average bond angle∠(O2,N2,C4) between O2, N2 and C4 is 109.140 with a standard deviationof 22.13°, a minimum value of 49.800 and a maximum value of 127.51°. Thetorsion angle ∠(O1,O2,N2,C4) as defined by O1, O2, N2 and C4 is 118.880with a standard deviation of 15.36°, a minimum value of 103.260 and amaximum value of 145.41°.

CA5 has an average distance (d(N2,CA5)) of 4.939 to N2 with a standarddeviation of 0.623, a minimum value of 3.723 Å and a maximum value of6.599 Å. The standard bond angle ∠(CA5,N2,O2) between CA5, N2 and O2 is152.850 with a standard deviation of 12.41°, a minimum value of 111.73°and a maximum value of 161.77°. The average torsion angle∠(O1,O2,N2,CA5) as defined by O1, O2, N2 and CA5 is 113.480 with astandard deviation of 68.44°, a minimum value of −161.98° and a maximumvalue of 148.15°. The average distance d(N2,CA2) between CA2 and N2 is5.909 Å with a standard deviation of 0.414 Å, a minimum value of 5.064 Åand a maximum value of 8.317 Å. The average bond angle ∠(CA2,N2,O2)between CA2, N2 and O2 is 155.190 with a standard deviation of 2.86°, aminimum value of 145.050 and a maximum value of 163.85°. The averagetorsion angle ∠(O1,O2,N2,CA2) as defined by O1, O2, N2 and CA2 is114.960 with a standard deviation of 55.79°, a minimum value of −157.89°and a maximum value of 159.770.

The average distance d(N2,CA4) between CA4 and N2 is 7.669 Å with astandard deviation of 0.620 Å, a minimum value of 6.056 Å and a maximumvalue of 8.240 Å. The average bond angle ∠(CA4,N2,O2) between CA4, N2and O2 is 160.71° with a standard deviation of 2.46°, a minimum value of154.82° and a maximum value of 164.21°. The average torsion angle∠(O1,O2,N2,CA4) as defined by O1, O2, N2 and CA4 is 113.64° with astandard deviation of 14.37°, a minimum value of 101.00° and a maximumvalue of 155.91°.

The average distance d(N2, C6) between C6 and N2 is 6.993 Å with astandard deviation of 1.011 Å, a minimum value of 5.556 Å and a maximumvalue of 8.271 Å. The average bond angle ∠(C6,N2,O2) between C2, N2 andO2 is 102.26° with a standard deviation of 9.84°, a minimum value of88.59° and a maximum value of 115.79°. The average torsion angle∠(O1,O2,N2,C6) as defined by O1, O2, N2 and C6 is 143.73° with astandard deviation of 4.82°, a minimum value of 137.30° and a maximumvalue of 150.07°.

Compounds can also match one or more of the features in anotherpharmacophore cluster in the RM region (Table 27, FIGS. 66, 72-75 ).This pharmacophore cluster consists of an aromatic ring CA3, thehydrogen bond accepting group O3 and the hydrogen bond donating groupH1.

The average distance d(N2,CA3) between N2 and CA3 is 5.057 Å with astandard deviation of 0.668 Å, a minimum value of 3.779 Å and a maximumvalue of 5.595 Å. The average bond angle ∠(O2,N2,CA3) between O2, N2 andCA3 is 157.18° with a standard deviation of 3.95°, a minimum value of151.660 and a maximum value of 161.48°. The average torsion angle∠(O1,O2,N2,CA3) as defined by O1, O2, N2 and CA3 is −13.65° with astandard deviation of 20.56°, a minimum value of −34.52°, and maximumvalue of 24.87°.

The average distance d(N2,O3) between O3 and N2 is 8.488 Å with astandard deviation of 0.670 Å, a minimum value of 7.778 Å and a maximumvalue of 9.724 Å. The average bond angle ∠(O3,N2,O2) between O3, N2 andO2 is 166.020 with a standard deviation of 2.30°, a minimum value of162.760 and a maximum value of 168.41°. The average torsion angle∠(O1,O2,N2,O3) as defined by O1, O2, N2 and O3 is −25.81° with astandard deviation of 57.02°, a minimum value of −144.09° and a maximumvalue of 43.95°.

The average distance d(N2,H1) between H1 and N2 is 8.663 Å with astandard deviation of 0.021 Å, a minimum value of 8.642 Å and a maximumvalue of 8.684 Å. The average bond angle ∠(H1,N2,O2) between H1, N2 andO2 is 168.740 with a standard deviation of 0.08°, a minimum value of168.660 and a maximum value of 168.81°. The average torsion angle∠(O1,O2,N2,H1) as defined by O1, O2, N2 and H1 is −16.54° with astandard deviation of 0.57°, a minimum of −17.10°, and maximum value of−16.97°. The pharmacophore model is illustrated by the FIG. 66-75 .

FIG. 66 is a schematic representation of the pharmacophore model relatedto elements of the binding site in its entirety. In subsequent figures,only parts of the subsection are shown for clarity.

FIG. 67 is a depiction of the distances between pharmacophore elementsdescribing the S1 and S2 regions. The S2 region comprises H4, O1, O2 andCA6. The S1 region area consists of H2, O4, CA1, C3, C5, C7, and N1.Distances mentioned in the text are shown.

FIG. 68 is a depiction of the angles between the pharmacophore elementsdescribing the S1 and S2 region. The S2 region comprises H4, O1, O2 andCA6. The S1 region consists of H2, O4, CA1, C3, C5, C7, and N1. Bondangles mentioned in the text are shown. Region definitions are omittedfor clarity reasons.

FIG. 69 is a depiction of the definitions of torsion angles used in thetext. The torsion angle is formed by 3 consecutive vectors and isdefined as the angle of the two outer vectors with arrow heads at theirend. Region definitions are omitted for clarity reasons.

FIG. 70 is a depiction of the definitions of torsion angles used in thetext. The torsion angle is formed by 3 consecutive vectors and isdefined as the angle of the two outer vectors with arrow heads at theirend. Region definitions are omitted for clarity reasons.

FIG. 71 is a depiction of the definitions of torsion angles used in thetext. The torsion angle is formed by 3 consecutive vectors and isdefined as the angle of the two outer vectors with arrow heads at theirend. Region definitions are omitted for clarity reasons.

FIG. 72 is a depiction of the distances between pharmacophore elementsdescribing the S2, S4 and RM region. The S2 region comprises H4, O1, O2and CA6. The S4 region consists of H3, N2, C2, C4, CA5, CA2, CA4, C6.The RM region comprises CA3, H1, O3. Distances mentioned in the text areshown.

FIG. 73 is a depiction of bond angles mentioned in the text. Regiondefinitions are omitted for clarity reasons.

FIG. 74 is a depiction of the definitions of torsion angles used in thetext. The torsion angle is formed by 3 consecutive vectors and isdefined as the angle of the two outer vectors with arrow heads at theirend. Region definitions are omitted for clarity reasons.

FIG. 75 is a depiction of torsion angles used in the text. The torsionangle is formed by 3 consecutive vectors and is defined as the angle ofthe two outer vectors with arrow heads at their end. Region definitionsare omitted for clarity reasons.

Without being limited by any theory, it is understood that certainpharmacophore elements may interact with particular elements of theMASP-2 binding site. The interactions that are considered to be the moreimportant interactions are discussed below. The S2 region pharmacophoreelements (Table 27) are understood to form classical hydrogen bondinteractions with the S4 shelf in the MASP-2 binding site. The averagedistance between H4 and the O atom in SER 654 is 2.308 Å with a standarddeviation of 0.157, a minimum value of 2.037 Å and a maximum value of2.787 Å. The average distance between O2 and the H atom in GLY 656 is2.425 Å with a standard deviation of 0.159 Å, a minimum value of 2.027 Åand a maximum value of 2.943 Å. The average distance between CA6 and theHZ atom in PHE 529 is 3.243 Å with a standard deviation of 0.263 Å, aminimum value of 2.558 Å and a maximum value of 4.535 Å.

Pharmacophore element C3 in the S1 region (FIG. 67 , Table 27) isunderstood to form a hydrophobic interaction with VAL 653 based on theshortest average distance of 2.762 Å. The standard deviation is 0.147 Å,the minimum value is 1.963 Å and the maximum value is 3.038 Å. Based onthe nature of C5 in the S1 region it can form with TYR 669 api-interaction. The shortest average distance is 3.701 Å with a standarddeviation of 0.246 Å, a minimum value of 1.820 Å, and maximum value of4.327 Å.

The aromatic ring pharmacophore group CA1 is understood to forminteractions with GLY 656. The shortest average distance is 3.494 Å witha standard deviation of 0.283 Å, a minimum value of 3.001 Å and amaximum value of 4.517 Å. CA1 interacts also with TRP 655 as exemplifiedby the shortest average distance with HA. The shortest average distanceis 3.563 Å, with a standard deviation of 0.142 Å, a minimum value of3.220 Å and a maximum value of 3.955 Å. CA1 interacts also with CYS 629.The shortest average distance is 3.051 Å with a standard deviation of0.178 Å, a minimum value of 2.199 Å, and maximum value of 3.620 Å.

The protonatable group N1 is understood to form an ionic interactionwith ASP 627. The shortest average distance is 3.750 Å, with a standarddeviation of 0.633 Å, a minimum value of 2.670 Å, and maximum value of5.269 Å.

The hydrophobic pharmacophore element C7 is understood to forminteractions with CYS 660. The shortest average distance is 2.438 Å witha standard deviation of 0.332 Å, a minimum value of 1.070 Å and maximumvalue of 3.816 Å. C7 is also understood for form an interaction with GLY656. The shortest average distance is 3.400 Å with a standard deviationof 0.298 Å, a minimum value of 2.707 Å and maximum value of 4.358 Å. Itis understood that C7 can also contact with SER 657. The shortestaverage distance is 2.873 Å with a standard deviation of 0.228 Å, aminimum value of 2.384 Å, and maximum value of 3.497 Å. C7 formscontacts with ASP 627. The shortest average distance is 3.411 Å with astandard deviation of 0.570 Å, a minimum value of 2.634 Å, and maximumvalue of 5.201 Å. It is understood that C7 can also interact with SER628. The shortest average distance is 3.623 Å with a standard deviationof 0.215 Å, a minimum value of 3.136 Å, and a maximum value of 5.000 Å.Furthermore, C7 can also interact with CYS 629. The shortest averagedistance is 3.495 Å, a standard deviation of 0.197 Å, a minimum value of2.608 Å, and a maximum value of 3.889 Å.

The hydrogen acceptor O4 is understood to form interactions with ARG630. The shortest average distance is 3.187 Å, with a standard deviationof 0.366 Å, a minimum value of 2.071 Å, and maximum value of 4.572 Å. O4may also form interactions with CYS 629. The shortest average distanceis 3.311 Å with a standard deviation of 0.156 Å, a minimum value of2.756, and a maximum value of 3.746 Å.

In the S3 region (Table 27, FIG. 72 ) it is understood that thepharmacophore element N2 forms a hydrogen bond with O of GLY 656. Theaverage distance is 2.771 Å with a standard deviation of 0.242 Å, aminimum value of 2.184 Å and a maximum value of 3.695 Å.

It is understood that the pharmacophore element H3 forms a hydrogen bondwith O of GLY 656. The average distance is 2.612 Å with a standarddeviation of 0.236 Å, a minimum value of 1.956 Å, and maximum value of3.613.

In the S4 region, it is understood that the pharmacophore element CA2forms aromatic pi interactions with PHE 529. The shortest averagedistance is 3.136 Å with a standard deviation of 0.295 Å, a minimum of2.490 and a maximum distance of 3.838 Å. It is understood that CA2 alsoforms hydrophobic interactions with PRO 608. The shortest averagedistance is 3.561 Å, with a standard deviation of 0.545, a minimum valueof 2.400 Å and a maximum value of 4.978 Å. It is further understood thatCA2 also forms hydrophobic interactions with TYR 607. The shortestaverage distance id 3.617 Å with a standard deviation of 0.437 Å, aminimum value of 2.644 Å, and a maximum value of 4.896 Å.

It is understood that the aromatic ring CA4 forms hydrophobicinteractions with GLY 528. The shortest average distance is 3.182 Å,with a standard deviation of 0.215 Å, a minimum value of 2.235 Å, and amaximum value of 3.450 Å. CA4 also forms hydrophobic interactions withPRO 608. The shortest average distance is 3.514 Å with a standarddeviation of 0.681 Å, a minimum value of 2.077 Å and a maximum value of5.235 Å. CA4 form aromatic pi interactions with PHE 529. The shortestaverage distance is 3.921 Å with a standard deviation of 0.237 Å, aminimum value of 3.306 Å, and a maximum value of 4.762 Å.

CA5 is understood to form hydrophobic interactions with TYR 607. Theshortest average distance is 3.520 Å, with a standard deviation of 0.419Å, a minimum value of 2.463 Å, and maximum value of 4.374 Å.

It is understood that C2 forms hydrophobic interactions with TYR 607.The shortest average distance is 3.621 Å with a standard deviation of0.449 Å, a minimum value of 2.780 Å, and maximum value of 5.630 Å. C2also is understood to form hydrophobic interactions with GLY 656. Theshortest average distance is 3.501 Å, with a standard deviation of 0.247Å, a minimum value of 2.920 Å, and maximum value of 4.091 Å.Furthermore, it is understood that C2 can interact with TRP 655. Theshortest average distance is 3.888 Å, with a standard deviation of 0.185Å, a minimum value of 3.090 Å, and maximum value of 4.320 Å.

C4 is understood to form hydrophobic interactions with PRO 608. Theshortest average distance is 3.282 Å, with a standard deviation of 0.607Å, a minimum value of 2.206 Å, and a maximum value of 4.992 Å.

It is understood that C6 forms a hydrophobic interaction with TRP 655.The shortest average distance is 3.698 Å, with a standard deviation of0.231 Å, a minimum value of 3.087 Å, and maximum value of 4.113 Å.Furthermore, it is understood that C6 forms hydrophobic interactionswith PHE 529. The shortest average distance is 3.006 Å, with a standarddeviation of 0.251 Å, a minimum value of 2.420, and a maximum value of3.836 Å. It is understood that C6 also interacts with SER 611. Theshortest average distance is 2.603 Å, with a standard deviation of 0.298Å, a minimum value of 1.991 Å, and a maximum value of 3.322 Å. C6 isalso understood to form hydrophobic interactions with PRO 608. Theshortest average distance is 3.835 Å, with a standard deviation of 0.360Å, a minimum value of 2.970 Å, and a maximum value of 4.919 Å. C6 canalso form hydrophobic interactions with GLY 528. The shortest averagedistance is 3.610 Å, with a standard deviation of 0.213 Å, a minimumvalue of 2.993 Å, and a maximum value of 4.666 Å.

In the RM region, it is understood that CA3 forms a hydrophobicinteraction with MET 658. The shortest average distance is 2.533 Å, witha standard deviation of 0.472 Å, a minimum value of 1.072 Å, and amaximum value of 3.890 Å. It is understood that CA3 also formsinteractions with ARG 630. The shortest average distance is 2.861 Å,with a standard deviation of 0.958 Å, a minimum value of 0.155 Å, and amaximum value of 5.371 Å.

It is understood that O3 also forms interactions with ARG 630. Theshortest average distance is 3.766, with a standard deviation of 0.893Å, a minimum value of 1.734 Å, and a maximum value of 5.839 Å.

Finally, it is understood H1 forms interactions with MET 658. Theshortest average distance is 3.371 Å, with a standard deviation of 0.510Å, a minimum value of 0.739 Å, and maximum value of 5.284 Å.

A small molecule compound can be evaluated in accordance with themethods described herein to determine matching with pharmacophoreelements as described herein by determining low energy conformations ofthe compound using molecular mechanics calculations or othercomputational methods. In addition, or alternatively, conformations canbe identified in accordance with methods described herein, or otherwise,by docking compounds to any MASP-2 structure derived by any theoreticalor experimental method such as homology modelling, comparative modellingor ab initio modeling, or such as X-ray diffraction or cryo electronmicroscopy. For example, 1Q3X is a SP-CCP2 human MASP-2 structure whichcould be used for docking, or a MASP-2 homology model obtained from aMASP-1 crystal structure used as structural template, in accordance withthe teachins of the present disclosure. Once conformations of themolecule have been identified, as disclosed herein, the compound can beevaluated as disclosed herein for a match to the parameters of thepharmacophore model as described above. The matching may be performedusing standard software known to the person having skill in the art suchas the tools available in the Discovery Suite available fromSchrödinger, LLC or other commercially available molecular modellingsoftware.

H. Compounds Defined by Reference to Computationally-Derived BindingRules

The present disclosure provides compounds with MASP-2 inhibitoryactivity, wherein the compound interacts with a binding site of MASP-2.The binding site(s) on the MASP-2 protein are identified using themethods described herein. The compounds of the disclosure interact withamino acids residues of the binding site. By identifying the bindingsites and ways the compounds of the disclosure interact with a bindingsite such as surface amino acid residues, it is possible to design a setof “binding rules” or “rule set” by which a MASP-2 inhibitor can also bespecifically described. By using a variety of compounds, including thosedisclosed herein, the rule set describes the compounds with completespecificity. In other words, by identifying such amino acids and how theinhibitor interacts with the amino acids, it is possible to specificallydefine the inhibitor itself.

In one embodiment, the present disclosure provides a method fordetermining virtual binding sites and thereby providing virtual bindingsites of the MASP-2 protein. As will be apparent herein, the newlyidentified binding sites provide an alternative method to structurallydescribe MASP-2 inhibitors by describing the structural interactionsbetween the inhibitory compounds and MASP-2 interactions, all inaccordance with the present disclosure.

The methods described herein involve one or more computationalexperiments (i.e., in silico docking methods or virtual docking methods)used in accordance with the present disclosure to model the interactionbetween MASP-2 protein surface residues, which have been derived fromexperimental crystallographic structure information, and known MASP-2small molecule inhibitors. Such virtual or in silico docking methodsidentify binding sites of MASP-2 and their interaction with smallmolecule inhibitors. In certain aspects of the present disclosure, theidentity of amino acids and their respective atoms on the proteinsurface that are accessible to small molecule binding often contributesignificantly to the overall binding energy (Fernández-Recio et al.,Comput Mol Sci, 680-698, 2011).

The series of computational experiments that employ experimentalcrystallographic structure information with known inhibitors providesvirtual binding sites, or three-dimensional models of their interactionwith MASP-2.

The virtual binding or docking methods described herein, allow foridentification of the amino acids that interact with the inhibitor. Byidentifying such amino acids and how the inhibitor interacts inaccordance with the present disclosure, it is possible to specificallydefine and describe the inhibitor itself.

In certain aspects, the inhibitor is a reversible inhibitor, anirreversible inhibitor which is covalently bound or alternatively, areversible covalently bound inhibitor. In certain aspects, theinhibitors herein are designed to interact with their biological targetsunder equilibrium binding conditions, wherein the desired drug-proteininteraction is a rapid and reversible process. In other aspects, theinhibitor is a covalent inhibitor, which is designed to bind to aprotein binding site through traditional reversible interactions, butalso undergo a covalent bond-forming event that produces a durabledrug-protein linkage. In yet other aspects, the inhibitors herein canform reversible covalent bonds with their respective binding sitetargets.

In certain aspects, the inhibitors herein are covalent inhibitors. Incontrast to conventional reversible drugs, irreversible inhibitorsachieve complete neutralization of their bimolecular targets such asMASP-2 given enough time. Covalent inhibitors have high biochemicalefficiencies and therefore have lower doses and reduced frequency ofdosing. In addition, covalent inhibitors have lower or reducedoff-target effects. In addition, in certain instances, the covalentinhibitors herein overcome competing endogenous substrates as they bindto the same target. Moreover, covalent inhibitors reduce the amount ofdrug resistance. Advantageously, covalent inhibitors address alternativeprotein binding site targets that can be shallow and thereforepreviously believed to be undrugable sites.

In certain aspects, the inhibitors herein are boron containing proteaseinhibitors. (see, Smoum et al. Chem. Rev. 2012, 112, 4156-4220). Forexample, peptidyl boronic acids are among the most potent inhibitors ofserine proteases known, achieving sub-nanomolar affinity frominteraction with the S-subsites alone. As one example,MeO-Suc-Ala-Ala-ProboroPhe-OH inhibited α-chymotrypsin with a K_(i)value of 0.16 nM. In certain instances, the inhibitors arefunctionalized aryl boronic acid derivatives.

In still yet other aspects, the inhibitors herein are derivatives ofisatoic anhydrides, oxazinediones and benzoxazinones. (see, Gelb et al.J Med Chem., 1986, 29, 585-589). These derivatives are generallyirreversible inhibitors. Further, other irreversible inhibitors aredesigned by taking a good reversible inhibitor herein and attaching areactive warhead to that structure such as an alkylating agent. Forexample, diazo compounds or haloketones can be used as warheads. Otherstrategies use X-ray crystallography and the co-crystals describedherein. Moieties that form covalent bonds are installed using theco-crystal structures (see, Power et al. Chem Rev. 2002, 102,4639-4750).

In certain aspects, the inhibitors herein are zinc mediated inhibitorssuch as derivatives of bis(5-amidino-2-benzimidazolyl)methane (BABIM)(see, Katz et al. Nature, Vol. 391. February 1998, p. 608-612). Incertain instances, the MASP-2 protein is inhibited by a coordinatingZn²⁺ in the presence of BABIM-like chelators, and is susceptible topotent Zn²⁺-mediated inhibition.

In certain aspects, the inhibitors are irreversible protease inhibitorscomprising electrophilic warheads such as aldehydes, boronates andα-keto functionalities. (see, Lin et al. Infectious Disorders—DrugTargets, 2006 6, 3-16).

1. Methods to Identify Virtual Binding Sites Step 1—Prepare InitialMASP-2 Models

Turning now to FIG. 76 , in order to identify and characterize a bindingsite on MASP-2, in certain aspects, multiple models of MASP-2 areprepared. In some aspects, multiple MASP-2 models are prepared bycomputationally reproducing experimental crystallographic structures.

In certain aspects, a modified MolSite approach (Fukunishi and Nakamura,Protein Science, 20, 95-106, 2011) is used to produce MASP-2 proteinmodels. The MolSite approach has been shown to correctly predict bindingsites with about 80-99% accuracy. For the purposes of the instantdisclosure, the MolSite method is modified by employing crystallographicMASP-2 structures to identify in silico those interacting residues thathave a propensity for ligand binding, such as small molecule binding asestablished by the crystallographic data.

As shown in FIG. 76 , in certain aspects, the present disclosurecomputationally reproduces the experimental crystallographic structuresof small molecules interacting with particular amino acid residueswithin a MASP-2 binding site (step 101). The MASP-2 protein models canbe computationally derived from the crystallographic data and thereafterverified via RMSD (root mean square deviation) superimposition on therespective crystal structures. In some aspects, initial MASP-2 proteinmodels are derived by computationally reproducing each of thecrystallographically derived MASP-2-bound small molecule inhibitorco-crystals (see, FIG. 1-57 ). In some embodiments, the secondcomplement control protein module (CCP2) chain, all solvent and watermolecules, counter ions, and the bound inhibitor molecule are removedfrom the crystallographic parameters prior to computationally derivingthe initial MASP-2 protein models. In some aspects, initial MASP-2protein models are derived by computationally reproducing each of thecrystallographically derived MASP-2-bound small molecule inhibitorco-crystals (FIG. 1-57 ), followed by removing the second complementcontrol protein module (CCP2) chain, all solvent and water molecules,counter ions, and the bound inhibitor molecule from the MASP-2 modelparameters. The docking parameters from these initial MASP-2 models arethen optimized in the next step.

Step 2—Prepare Optimized MASP-2 Models

Next, the docking parameters of the initial MASP-2 models are optimizedby adding polar hydrogens, employing energy minimization algorithmsusing a force field, followed by assigning charges to protein atoms(AMBER) and using manual inspection and correction (step 110). Solventmolecules can be added back to locations where such molecules areobserved crystallographically. In some aspects, all water molecule areadded back to locations where such molecules are observedcrystallographically. In some aspects, the CCP2 chain is optionallyadded back to the crystallographically observed location. Furtheradjustments are then made to account for dipoles without altering netcharges on any residues. A plurality or multiple MASP-2 protein modelsare produced from the optimization step to account for conformationaldifferences observed in the crystallographic co-structures of MASP-2. Asmentioned above, this disclosure describes 57 co-crystals with smallmolecule inhibitors. Each optimized MASP-2 model with optimized andMASP-2 specific docking parameters is used in successive virtual dockingprocesses or campaigns (i.e., computational docking experiments)including, re-docking of the crystallographically observed smallmolecule inhibitor and cross-docking of the small molecules selectedfrom the small molecule library. The fidelity of the outcome of suchcross- and re-docking experiments will inform the optimization of theMASP-2 model and docking parameters.

Step 3—Prepare Small Molecule Library

In certain aspects, a database is populated with digital representationsof small molecules known to inhibit the activity of MASP-2 (for example,compounds selected from Tables 28 or 31) (see, step 131). The digitalrepresentations of each small molecule within the library are energyminimized three dimensional structures of the small molecules that areproduced using known computational methods. In some aspects, thecrystallographically observed small molecule inhibitors of each of the57 co-crystals are computationally reproduced as energy minimized threedimensional structures using known computational methods. Suchcomputational algorithms involve the identification of ionizable andpolarizable groups within each small molecule structure, and renderingdigital representations of each small molecule in both a charged stateand a neutral state, and with and without, or only a subset ofcrystallographically identified bound solvent molecules.

The small molecule library includes ligands which are known to bind toMASP-2 as well as molecules that do not bind to MASP-2. The smallmolecules that are known to inhibit MASP-2 (i.e., bind to MASP-2) arereferred to as “hits.” The small molecules that do not exhibit anyMASP-2 inhibitory activity (i.e., known to not bind to or inhibitMASP-2) are referred to as “decoys.” The docking behavior of both thehits and the decoys included in the database are thereafter assessed inthe next step (step 4) of the method.

Step 4—Virtual Docking

In certain aspects, software such as GLIDE software (Friesner et al.,2016; Schrödinger, LLC) can be used to carry out rigid as well asflexible computational docking of small molecules onto each MASP-2 model(step 152). As used herein, the term “cross-docking” refers to thecomputational docking of a compound selected from the set of 57 MASP-2crystallographic co-structures onto two or more MASP-2 models, thelatter of which being different from the MASP-2 model derived with thatbound small molecule. The term “re-docking” refers to the computationaldocking of the crystallographically observed small molecule inhibitorrepresentation back onto the same MASP-2 model which was derived fromits corresponding co-crystal structure. In these virtual dockingprocesses or campaigns, the docking experiments are limited to exposedresidues on the surface only. Resulting docked ligand positions arethereafter sampled, scored and binned and, assigned a distance cutoff tomatch ligand atoms to MASP-2 surface exposed atoms. For dockingcampaigns, primarily preferred surface sites are used, namely those thathave been identified crystallographically to bind, via hydrogen bondingand van der Waals contacts, certain small molecules. Such surface sitesare prone to binding of small molecules and hence this information isused to serve as anchor points for those small molecule compoundsselected from HTS hits (see Table 28).

In certain aspects, other software programs such as the following can beused in this step.

In certain aspects, ICM Pro software is used. (Abagyan & Totrov, Journalof Computational Chemistry, Volume 15, Issue 5, May 1994, Pages 488-506;and Abagyan et al., Journal of Molecular Biology Volume 235, Issue 3, 20Jan. 1994, Pages 983-1002).

In certain aspects, GRID is used which is described as follows:Protein-probe energies computed by Lennard-Jones, electrostatic andhydrogen bonding potentials are mapped onto a grid around the protein.(See, Goodford, P. J. A computational procedure for determiningenergetically favorable binding sites on biologically importantmacromolecules. J. Med. Chem., 1985, 28, 849-857).

In certain aspects, Pocket is used which is described as follows: A 3 Åprobe scans the protein along a Cartesian grid for line segments notoverlapping with protein but surrounded by overlapping segments. (See,Levitt, D. G.; Banaszak L. J. POCKET: a computer graphics method foridentifying and displaying protein cavities and their surrounding aminoacids. J. Mol. Graph., 1992, 10, 229-234).

In certain aspects, Delaney is used which is described as follows:Expansion and contraction of surface probes is used to detect pocketswhere probe particles concentrate. (See, Delaney, J. S. Finding andfilling protein cavities using cellular logic operations. J. Mol.Graph., 1992 10, 174-177).

In certain aspects, Del Carpio is used which is described as follows:Closest distances between the protein's center of gravity and proteinsurface points are used to identify pockets. (See, Del Carpio C. A.;Takahashi Y.; Sasaki S. A new approach to the automatic identificationof candidates for ligand receptor sites in proteins: (I). Search forpocket regions. J. Mol. Graph., 1993, 11, 23-29).

In certain aspects, VOIDOO is used which is described as follows:Cavities are detected by stepwise increase of Van-der-Waals radii of allprotein atoms. After a floodfill algorithm, sealed off localizations canbe identified as cavities. (See, Kleywegt, G. J.; Jones, T. A. EfficientRebuilding of Protein Structures. Acta Crystallogr. Sect. D: Biol.Crystallogr., 1994, 50, 178-185).

In certain aspects, SurfNet is used which is described as follows:Spheres between two atoms containing no other atoms are created andscanned for the cluster of spheres with the largest volume. (See,Laskowski, R. A. SURFNET: A program for visualizing molecular surfaces,cavities, and intermolecular interactions. J. Mol. Graph., 1995, 13,323-330).

In certain aspects, APROPOS is used which is described as follows:Protein pockets are determined employing an alpha-shape algorithm thatallows for a complete global envelope of the protein. (See, Peters, K.P.; Fauck, J.; Frömmel, C. The automatic search for ligand binding sitesin proteins of known three-dimensional structure using only geometriccriteria. J. Mol. Biol., 1996, 256, 201-213).

In certain aspects, LIGSITE is used which is described as follows: On aregular grid around the protein, lines are drawn from each grid pointalong the x/y/z-axis as well as the cubic diagonals. Segments of linesthat are enclosed by protein from both sides are considered as cavities.(See, Hendlich, M.; Rippmann, F.; Barnickel, G. LIGSITE: automatic andefficient detection of potential small-molecule binding sites inproteins. J. Mol. Graph. Model., 1997, 15, 359-363).

In certain aspects, Superstar is used which is described as follows:Creates propensity maps of basic molecular probes along the proteinsurface. (See, Verdonk, M. L.; Cole, J. C.; Taylor, R. SuperStar: aknowledge based approach for identifying interaction sites in proteins.J. Mol. Biol., 1999, 289, 1093-1108).

In certain aspects, PASS is used which is described as follows: Thealgorithm repeats filtering and expanding a set of initial probe sphereson the protein surface to eventually find “active site points” (See,Brady G. P.; Stouten P. F. Fast prediction and visualization of proteinbinding pockets with PASS. J. Comput. Aided Mol. Des., 2000, 14,383-401).

In certain aspects, ConSurf is used which is described as follows:Identifying functional sites on proteins by determining the conservationof sequence homologues. (See, Glaser, F.; Pupko, T.; Paz, I.; Bell, R.E.; Bechor-Shental, D.; Martz, E.; Ben-Tal, N. ConSurf: identificationof functional regions in proteins by surface-mapping of phylogeneticinformation. Bioinformatics, 2003, 19, 163-164).

In certain aspects, CASTp is used which is described as follows: Usesalpha shape theory and triangulation methods to predict pockets. (See,Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz with structuraland topographical mapping of functionally annotated residues. NucleicAcids Res., 2006, 34, W116-W118).

In certain aspects, LigandFit is used which is described as follows:Identifies possible binding sites using a flood-filling-algorithm anddocks ligands using a Monte Carlo conformational search (See,Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: anovel method for the shape-directed rapid docking of ligands to proteinactive sites. J. Mol. Graph. Model., 2003, 21, 289-307).

In certain aspects, Q-SiteFinder is used which is described as follows:Energetically based method: clusters of protein surface regions thatshow favorable Van der Waals interactions with a methyl-group arecollected and ranked (See, Laurie, A. T. R.; Jackson, R. M.Q-SiteFinder: an energy-based method for the prediction ofprotein-ligand binding sites. Bioinformatics, 2005, 21, 1908-1916).

In certain aspects, DrugSite is used which is described as follows:Predicts binding sites on the basis of Van der Waals potential gridpoint maps (See, An, J.; Totrov, M.; Abagyan, R. Pocketome viacomprehensive identification and classification of ligand bindingenvelopes. Mol. Cell. Proteomics, 2005, 4, 752-761).

In certain aspects, MEDock is used which is described as follows:Evolutionary algorithm utilizing the maximum entropy (ME) property ofthe Gaussian probability distribution (See, Chang, D. T.-H.; Oyang,Y.-J.; Lin, H.-H. MEDock: a web server for efficient prediction ofligand binding sites based on a novel optimization algorithm. NucleicAcids Res., 2005, 33, W233-W238).

In certain aspects, LIGSITEcsc is used which is described as follows: Inextension to the traditional LigSite method, the Connolly surface areais calculated and grid points are scanned for surface-solvent-surfaceevents. Additionally, the top three predicted pockets are re-rankedaccording to sequence conservation. (Huang, B.; Schroeder, M.LIGSITEcsc: predicting ligand binding sites using the Connolly surfaceand degree of conservation. BMC Struct. Biol., 2006, 6, 19).

In certain aspects, Screen/Mark-Us is used which is described asfollows: Cavities are geometrically determined via the differencebetween the molecular surface and the probe-specified molecular envelopeand statistical analysis. (See, Nayal, M.; Honig, B. On the nature ofcavities on protein surfaces: application to the identification ofdrug-binding sites. Proteins, 2006, 63, 892-906).

In certain aspects, Pocket-Picker is used which is described as follows:A rectangular grid is used to segregate relevant points along theprotein surface which are then clustered and ranked according to shapedescriptors. (See, Weisel, M.; Proschak, E.; Schneider, G. PocketPicker:analysis of ligand binding-sites with shape descriptors. Chem. Cent. J.,2007, 1, 7).

In certain aspects, Fuzzy-Oil-Drop is used which is described asfollows: Analyzes the protein for regions with high hydrophobicdeficiency, i.e. the difference between observed and idealizedhydrophobicity distribution declared by the ‘Fuzzy Oil Drop Model’ (See,Brylinski, M.; Prymula, K.; Jurkowski, W.; Kochanczyk, M.; Stawowczyk,E.; Konieczny, L.; Roterman, I. Prediction of functional sites based onthe fuzzy oil drop model. PLoS Comput. Biol., 2007, 3, e94).

In certain aspects, SiteMap is used which is described as follows: Setsof relevant points are identified by geometric and energetic means andanalyzed for hydrophobicity and other physicochemical properties (See,Halgren, T. New Method for Fast and Accurate Binding-site Identificationand Analysis. Chem. Biol. Drug Des., 2007, 69, 146-148).

In certain aspects, FINDSITE is used which is described as follows: Themethod uses protein threading to identify ligand bound templates whichare then superimposed and analyzed for similarities in the ligandbinding sites (See, Brylinski, M.; Skolnick, J. A threading-based method(FINDSITE) for ligand-binding for ligand-binding site prediction andfunctional annotation. PNAS, 2008, 105, 129-134).

Step 5—Designate Virtual Binding Sites

As shown in FIG. 76 , step 182, after visual inspection of suchidentified interaction sites, binding hot spots are grouped bynormalizing the docking score by the number of ligand atoms prior tosorting the pairings of ligand and site atom pairings. In addition,Volume and Enclosure (for example, as computed via MAESTRO, Schrödinger,LLC) of the interacting sites and rank clusters of such ligand/site atompairings as hot spots with respect to number and size of interactions.The highest ranked ligand/site atom pairing will be designated ‘virtualbinding site’ for each of the compounds in Table 28. Other compoundsfrom compound libraries with known MASP-2 inhibition activity describedbelow are also used.

TABLE 28 Compound Molecular MASP-2 Ki Thrombin Ki No. Chemical StructureWeight (μM) (μM)  1#

253.26 *** ***  2#

271.25 *** *  3#

388.22 * ***  4#

369.38 *** *  5#

285.32 ** **  6#

265.27 *** *  7#

296.29 *** ***  8

201.15 ** No Activity  9

300.27 *** *** 10

229.26 *** * 11

247.63 *** No Activity 12#

270.24 *** *** 13#

287.31 * No activity 14

268.23 *** *** 15

245.27 * No activity 16

410.73 * No activity 17#

412.45 *** * 18

271.71 *** *** 19#

301.34 *** * 20#

312.07 *** No Activity 21#

216.18 *** *** 22

310.68 ** No Activity 23

370.46 *** No Activity 24#

305.29 *** ** 25

305.29 * No activity 26#

163.13 *** * 27#

233.18 *** * 28

259.26 * No activity 29

248.26 *** * 30

257.29 * No activity 31#

401.40 *** No activity 32#

222.24 *** No activity 33

453.30 *** *** 34#

401.43 *** * 35

352.23 * * 36

314.08 *** * 37

231.25 * No activity 38

164.16 ** ** 39#

347.35 *** ** 40#

363/35 *** *** 41#

230.22 *** No activity 42#

275.30 *** * 43#

271.43 *** * 44#

351.32 *** * 45#

292.09 *** * 46

133.15 * No activity 47^(a)

135.17 * No activity 51

620.63 ** No activity 53

170.21 *** ** # = irreversible inhibitor; ^(a)HCl salt; ^(b)HCl hydratesalt; ^(c)HNO₃ salt Key: MASP-2 and Thrombin Inhibition *** (Ki < 10 μM)** (Ki: 10-25 μM) * (Ki: 25-100 μM)

In addition to the compounds of Table 28, it is possible to screen othercompound libraries for identification of binding sites. Certain of themolecular interaction data presented herein is derived from 57co-crystals of MASP-2 and specific inhibitors (see FIGS. 1-57 ).

In certain aspects, the NCI Diversity Set, which is a compoundcollection representing a universally diverse group of “drug-like” smallmolecules chosen on the basis of their three dimensional pharmacophoricscaffolds, which represent diverse, biologically relevant pharmacophoricscaffolds from within the NCI parent library is used.

In addition, the Chembridge library can also be screened. This libraryhas been selected from their master database of (>5 million compounds)ensuring computational diversity of the discrete chemical moieties,drug-like properties, as well as medicinal chemistry pharmacokinetics.

Moreover, the Maybridge library is another alternative collection thatis comprised of 60,000 organic compounds, produced by innovativesynthetic techniques, representing 400,000 pharmacophores identifiedwithin the world drug index.

Alternative compound libraries are available and a very recentcompilation of one million commercially accessible compounds, includinga natural product library, was made available for web-accessibledatabase searching and docking through ZINC(http://blaster.docking.org/zinc) DOCK Blaster is a public accessservice for structure-based ligand discovery.

In certain aspects, a ChemDiv library (12760High Bluff Drive, Suite 370,San Diego, Calif. 92130 USA) is used. The ChemDiv library offers a widevariety of compounds including more than 1.5 M individual solidscreening compounds.

In one aspect, parameters are controlled and adjusted to increase thefidelity of the above process by comparing computationally identifiedhot spots from those obtained crystallographically. Specifically, thebinding of decoy compounds and ligand/site atom pairings in the bindingpocket for inhibitors for which we have identified key residues andtheir respective ligand atom/site atom pairings to computed ligand/siteatom pairings are compared and used to assess the fidelity of theidentification of virtual binding sites.

2. Binding Sites

In some aspects, a virtual binding site identified on MASP-2 is at leastone amino acid residue of SEQ ID NO: 1. In some aspects, a virtualbinding site identified on MASP-2 is one amino acid residue to 100 aminoacid residues of SEQ ID NO: 1. In some aspects, a virtual binding siteidentified on MASP-2 is two to 90 amino acid residues of SEQ ID NO: 1,or three to 85, four to 80, five to 75, six to 70, seven to 65, eight to60, nine to 55, 10 to 50, 11 to 45, 12 to 40, 13 to 35, 14 to 30, or 15to 25 amino acid residues of SEQ ID NO: 1. In some aspects, a virtualbinding site identified on MASP-2 is five to 50 amino acid residues ofSEQ ID NO: 1, or five to 25, five to 20, five to 10, or 10 to 40, 10 to35, or 15 to 35 amino acid residues of SEQ ID NO: 1. In some aspects, avirtual binding site identified on MASP-2 is one amino acid residue ofSEQ ID NO: 1, or two, three, four, five, six, seven, eight, nine, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 35, 40, 45, or 50 amino acid residues of SEQ ID NO: 1. In someaspects, a virtual binding site identified on MASP-2 is about five to 30amino acid residues of SEQ ID NO: 1. In some aspects, a virtual bindingsite identified on MASP-2 is about 10 to 20 amino acid residues of SEQID NO: 1. In some aspects, a virtual binding site identified on MASP-2is about 10 amino acid residue of SEQ ID NO: 1.

In some aspects, one or more virtual binding sites are identified onMASP-2. In some embodiments, one to 100 virtual binding sites areidentified on MASP-2, or one to 40, one to 30, one to 25, one to 20, oneto 15, one to 10, or one to 5 (1, 2, 3, 4, 5) virtual binding sites areidentified on MASP-2. In some embodiments, one virtual binding site isidentified on MASP-2. In some embodiments, two virtual binding sites areidentified on MASP-2, or three, four, five, six, seven, eight, nine, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, or 50virtual binding sites are identified on MASP-2.

In some aspects, the amino acids of the MASP-2 virtual binding sites arehydrophobic, hydrophilic, or a mixture thereof. In some aspects, theamino acids are of the MASP-2 virtual binding site are hydrophobic. Insome aspects, the amino acids of the MASP-2 virtual binding sites arehydrophilic. In some aspects, the amino acids of the MASP-2 virtualbinding sites are a mixture of hydrophobic and hydrophilic amino acidresidues.

In some aspects, the MASP-2 virtual binding sites contain one or morehydrophobic amino acid residues. In some aspects, the one or morehydrophobic amino acid residues are two or more hydrophobic amino acidresidues, three or more hydrophobic amino acid residues, four or morehydrophobic amino acid residues, five or more hydrophobic amino acidresidues, six or more hydrophobic amino acid residues, seven or morehydrophobic amino acid residues, eight or more hydrophobic amino acidresidues, nine or more hydrophobic amino acid residues, 10 or morehydrophobic amino acid residues, 11 or more hydrophobic amino acidresidues, 12 or more hydrophobic amino acid residues, 13 or morehydrophobic amino acid residues, 14 or more hydrophobic amino acidresidues, 15 or more hydrophobic amino acid residues, 20 or morehydrophobic amino acid residues, or 25 or more hydrophobic amino acids.

In some aspects, the MASP-2 virtual binding sites contain one or morehydrophilic amino acid residues. In some aspects, the one or morehydrophilic amino acid residues are two or more hydrophilic amino acidresidues, three or more hydrophilic amino acid residues, four or morehydrophilic amino acid residues, five or more hydrophilic amino acidresidues, six or more hydrophilic amino acid residues, seven or morehydrophilic amino acid residues, eight or more hydrophilic amino acidresidues, nine or more hydrophilic amino acid residues, 10 or morehydrophilic amino acid residues, 11 or more hydrophilic amino acidresidues, 12 or more hydrophilic amino acid residues, 13 or morehydrophilic amino acid residues, 14 or more hydrophilic amino acidresidues, 15 or more hydrophilic amino acid residues, 20 or morehydrophilic amino acid residues, or 25 or more hydrophilic amino acids.

In some aspects, a virtual binding site identified on MASP-2 is at leastone amino acid residue selected from the MET 1 to LYS 350 region of SEQID NO: 1. In some aspects, a virtual binding site identified on MASP-2is at least one amino acid residue selected from the ASP 351 to PHE 686region of SEQ ID NO: 1. In some aspects, a virtual binding siteidentified on MASP-2 is at least one amino acid residue selected fromthe MET 1 to LYS 350 region of SEQ ID NO: 1 and at least one amino acidresidue selected from the ASP 351 to PHE 686 region of SEQ ID NO: 1. Insome aspects, a virtual binding site identified on MASP-2 is at leastone amino acid residue selected from the MET1 to THR50 region of SEQ IDNO: 1, or the ALA 51 to ALA 100 region, PRO 101 to PRO 150, THR 151 toGLU 200, TYR 201 to THR 250, ASP 251 to CYS 300, PRO 301 to LYS 350, ASP351 to PHE 400, TYR 401 to LYS 450, ALA 451 to GLY 500, THR 501 to PRO550, ILE 551 to ALA 600, ALA 601 to GLY 650, the GLY 651 to PHE 686region of SEQ ID NO: 1, or combinations thereof.

In some aspects, the one or more virtual binding sites identified onMASP-2 are one or more of the residues of the of the serine proteasedomain residues 445-686 of SEQ ID NO: 1. In one aspect, one or more ofthe catalytic triad is included, HIS 483, ASP 532 and SER 633.

In some aspects, the one or more virtual binding sites identified onMASP-2 are one or more of the following residues: LEU 621, ALA 663, GLY664, TYR 666, VAL 429, CYS 430, GLU 431, PRO 432, VAL 433, CYS 434, ILE544, ASN 545, ALA 527, GLY 528, GLU 378, ARG 376, GLU 397, GLU 398, ASP475, SER 374, LEU 473, TYR 474, PRO 550, ILE 551, CYS 552, LYS 541, VAL542, VAL 543, ILE 544, ASN 545, SER 546, ASN 547, ILE 548, THR 549, GLY574, ILE 363, THR 440, THR 441, PHE 400, TYR 401, ASP 532, ASP 526, HIS525, TYR 523, THR 466, ILE 661, GLU 662, LEU 575, PRO 605, VAL 485, TYR486, GLU 487, GLN 488, LYS 489, HIS 490, GLY 631, LEU 581, THR 467, GLY667, SER 657, GLY 656, TRP 655, SER 654, SER 633, ARG 630, CYS 629, SER628, ASP 627, PHE 529, HIS 483, PRO 606, PRO 608, SER 611, VAL 653, MET658, TYR 669, TYR 607, ASN 659, CYS 660, GLN 665, and combinationsthereof. In some aspects, the one or more virtual binding sitesidentified on MASP-2 are one or more of the following residues: LEU 621,ALA 663, GLY 664, TYR 666, VAL 429, CYS 430, GLU 431, PRO 432, VAL 433,CYS 434, ILE 544, ASN 545, ALA 527, GLY 528, GLU 378, ARG 376, GLU 397,GLU 398, ASP 475, SER 374, LEU 473, TYR 474, PRO 550, ILE 551, CYS 552,LYS 541, VAL 542, VAL 543, ILE 544, ASN 545, SER 546, ASN 547, ILE 548,THR 549, GLY 574, ILE 363, THR 440, THR 441, PHE 400, TYR 401, ASP 532,ASP 526, HIS 525, TYR 523, THR 466, ILE 661, GLU 662, LEU 575, PRO 605,VAL 485, TYR 486, GLU 487, GLN 488, LYS 489, HIS 490, GLY 631, LEU 581,THR 467, and combinations thereof. In some aspects, the one or morevirtual binding sites identified on MASP-2 are one or more of thefollowing residues: GLY 667, SER 657, GLY 656, TRP 655, SER 654, SER633, ARG 630, CYS 629, SER 628, ASP 627, PHE 529, HIS 483, PRO 606, PRO608, SER 611, VAL 653, MET 658, TYR 669, TYR 607, ASN 659, CYS 660, GLN665, and combinations thereof.

In some aspects, proteins interact with small molecules on their surfaceand when strongly bound, can be resolved crystallographically. Suchsmall molecules often originate from buffer components orcryoprotectants that are added to the protein sample to aidcrystallization or protein crystal cryo-protection. Usingcrystallographic structures of MASP-2 with bound compounds (see, FIG.1-57 ), a number of such small molecules bound to MASP-2 (Tables 29 andTable 30) have been identified, such as polyethylene glycol (PEG),succinic acid (SIN), sulfate (SO₄), glycerol (GOL),2-methyl-2,4-pentanediol (MPD), phosphate (PO₄), acetic acid (ACT) aswell as ligand (LIG) molecules that are bound at a location that isdifferent from the canonical binding site and away from the active site.The hydrogen bonding pattern, as well as their van der Waals interactionpattern with MASP-2 surface atoms may be of utility in identifyingbinding sites for inhibitor molecules. MASP-2 amino acids and theirrespective experimentally determined hydrogen bond forming residues andatoms are listed in Table 29, which shows the hydrogen bonding patternof MASP-2 serine protease residues and corresponding atoms with smallmolecules. Hydrogen bond donor and acceptor distances are provided, aswell as the respective residue identity and corresponding numbering. Inshort, such H-bond forming amino acids constitute THR 466, HIS 483, GLU487, TYR 523, GLY 528, LYS 541, ARG 578, ARG 583, ASN 584, ARG 630, GLY631, SER 633, THR 644 and MET 658. Likewise, MASP-2 amino acids andspecific atoms therein that form van der Waals with such small moleculesare listed in Table 30. In short, such van der Waals contact formingamino acids include GLY465, THR466, THR467, ALA468, TYR474, ASN476,HIS483, GLU487, ASP526, GLY528, PHE529, CYS552, LEU575, ARG 578, GLY579,LEU581, ALA582, ARG583, ASN584, MET586, PRO606, TYR607, PRO608, ARG630,GLY631, SER633, ASP641, THR644, ARG646, SER657, MET658, ALE683, SER684.

TABLE 29 Hydrogen bonding pattern of MASP-2 serine protease residues andcorresponding atoms with small molecules. Hydrogen bond donor andacceptor distances are provided, as well as the respective residueidentity and corresponding numbering. DONOR ACCEPTOR Compound SmallResidue or Residue or Distance No. molecule molecule # Atom molecule #Atom [Å] 1129 PEG LYS 541 NZ PEG 1 O4 2.87 1129 SIN MET 658 N SIN 1 O12.78 1059 SO4_1 SER 633 OG SO4 1 O3 3.15 1059 SO4_1 SER 633 OG SO4 1 O12.62 1059 SO4_1 GLY 631 N SO4 1 O1 2.88 1059 SO4_1 HIS 483 NE2 SO4 1 O32.61 1059 SO4_2 ASN 584 ND2 SO4 2 O1 3.11 1059 SO4_2 ASN 584 N SO4 2 O13.12 1059 SO4_2 ARG 583 NH2 SO4 2 O4 2.82 1059 SO4_2 ARG 583 NE SO4 2 O23.19 1059 SO4_2 ARG 583 N SO4 2 O2 2.86 1059 SO4_2 ARG 578 NH1 SO4 2 O32.51 1088 Lig2 LIG 2 N31 GLY 528 O 3.01 1088 Lig2 LIG 2 N29 GLY 528 O3.03 1088 Lig2 LIG 2 N31 TYR 523 OH 2.8 1088 Lig1 LIG 1 N31 GLU 487 OE23.02 1088 Lig1 LIG 1 N29 GLU 487 OE1 2.78 1065 MPD1 SER 633 OG MPD 1 O22.6 1065 MPD1 GLY 631 N MPD 1 O2 2.88 1030 SO4_1 ASN 584 ND2 SO4 1 O13.21 1030 SO4_1 ASN 584 N SO4 1 O1 3.04 1030 SO4_1 ARG 583 NH1 SO4 1 O42.92 1030 SO4_1 ARG 583 NE SO4 1 O2 3 1030 SO4_1 ARG 583 N SO4 1 O2 2.761030 SO4_1 ARG 578 NH2 SO4 1 O3 2 1030 SO4_2 SER 633 OG SO4 2 O1 2.521030 SO4_2 GLY 631 N SO4 2 O1 2.83 1030 SO4_2 ARG 630 NH2 SO4 2 O4 3.031030 SO4_2 ARG 630 NE SO4 2 O4 2.63 1030 SO4_2 HIS 483 NE2 SO4 2 O3 2.59melagatran ACT THR 644 OG1 ACT 1 OXT 2.67 1090 GOL SER 633 OG GOL 1 O12.5 1090 GOL GLY 631 N GOL 1 O1 3.32 1090 GOL THR 466 OG1 GOL 1 O2 2.841089 Lig2 Lig 2 N5 GLU 487 OE2 3 1089 Lig2 Lig 2 N4 GLU 487 OE1 2.661097 PO4_1 SER 633 OG PO4 1 O3 2.55 1097 PO4_1 GLY 631 N PO4 1 O3 2.851097 PO4_1 HIS 483 NE2 PO4 1 O1 2 1097 PO4_2 SER 633 OG PO4 2 O1 2.511097 PO4_2 GLY 631 N PO4 2 O1 2.92 1097 PO4_2 HIS 483 NE2 PO4 2 O4 3.031097 PO4_2 THR 466 OG1 PO4 2 O2 3.33 Abbreviations used: polyethyleneglycol (PEG), succinic acid (SIN), sulfate (SO₄), glycerol (GOL),2-methyl-2,4-pentanediol (MPD), phosphate (PO₄), acetic acid (ACT),surplus ligand (LIG) molecules.

TABLE 30 van der Waals contact pattern of MASP-2 serine proteaseresidues and corresponding atoms with small molecules. Inter atomiccontact distances are provided, as well as the respective residueidentity and corresponding numbering. Compound Small Distance No.molecule ATOM 1 ATOM 2 [Å] 1129 PEG PEG O1 SER 684 CA 3.58 1129 PEG PEGO2 ILE 683 CG2 3.78 1129 PEG PEG C1 ILE 683 CG2 3.81 1129 PEG PEG C1 ILE683 O 3.61 1129 PEG PEG C4 ASN 476 OD1 3.77 1129 PEG PEG C3 ASN 476 OD13.58 1129 PEG PEG O4 ASN 476 CG 3.55 1129 PEG PEG C4 TYR 474 CG 3.891129 PEG PEG C3 TYR 474 CG 3.75 1129 PEG PEG O4 TYR 474 CB 3.67 1129 PEGPEG C4 TYR 474 CB 3.79 1129 SIN SIN O3 MET 658 SD 3.75 1129 SIN SIN O3MET 658 CG 3.73 1129 SIN SIN O1 MET 658 CB 3.41 1129 SIN SIN O1 MET 658CA 3.71 1129 SIN SIN O1 SER 657 CB 3.58 1129 SIN SIN O1 SER 657 C 3.61129 SIN SIN O4 SER 657 C 3.88 1129 SIN SIN O1 SER 657 CA 3.49 1129 SINSIN C1 TYR 607 OH 3.25 1129 SIN SIN C3 TYR 607 OH 3.78 1129 SIN SIN O1TYR 607 CZ 3.9 1129 SIN SIN O2 PRO 606 CD 3.88 1129 SIN SIN C2 PRO 606CG 3.79 1129 SIN SIN C3 PRO 606 CG 3.62 1059 SO4_1 SO4 S SER 633 OG 3.481059 SO4_1 SO4 O3 SER 633 CB 3.88 1059 SO4_1 SO4 O1 SER 633 CB 3.38 1059SO4_1 SO4 O1 GLY 631 CA 3.86 1059 SO4_1 SO4 O1 ARG 630 C 3.59 1059 SO4_1SO4 O4 ARG 630 CG 3.25 1059 SO4_1 SO4 O1 ARG 630 CB 3.89 1059 SO4_1 SO4O4 ARG 630 CB 3.46 1059 SO4_1 SO4 O1 ARG 630 CA 3.32 1059 SO4_1 SO4 O3HIS 483 CD2 3.15 1059 SO4_1 SO4 O3 HIS 483 CE1 3.82 1059 SO4_2 SO4 O3MET 586 CE 3.63 1059 SO4_2 SO4 O1 MET 586 CE 3.1 1059 SO4_2 SO4 S MET586 CE 3.83 1059 SO4_2 SO4 O1 ASN 584 CG 3.74 1059 SO4_2 SO4 O1 ASN 584CB 3.44 1059 SO4_2 SO4 O1 ASN 584 CA 3.8 1059 SO4_2 SO4 S ARG 583 NH23.81 1059 SO4_2 SO4 O4 ARG 583 CZ 3.82 1059 SO4_2 SO4 O2 ARG 583 CG 3.771059 SO4_2 SO4 O2 ARG 583 CB 3.54 1059 SO4_2 SO4 O2 ARG 583 CA 3.79 1059SO4_2 SO4 S ARG 583 N 3.57 1059 SO4_2 SO4 O2 ALA 582 C 3.69 1059 SO4_2SO4 O1 ALA 582 C 3.89 1059 SO4_2 SO4 O1 ALA 582 CB 3.86 1059 SO4_2 SO4O3 ALA 582 CA 3.62 1059 SO4_2 SO4 O2 ALA 582 CA 3.63 1059 SO4_2 SO4 O1ALA 582 CA 3.86 1059 SO4_2 SO4 S ARG 578 NH1 3.56 1059 SO4_2 SO4 O3 ARG578 CZ 3.51 1059 PEG1 PEG C1 PRO 606 O 3.77 1059 PEG1 PEG C4 PRO 606 CG3.07 1059 PEG1 PEG C4 PRO 606 CB 3.83 1088 Lig2 LIG C15 GLY 631 CA 3.641088 Lig2 LIG C14 GLY 631 CA 3.8 1088 Lig2 LIG C15 GLY 631 N 3.57 1088Lig2 LIG C14 GLY 631 N 3.57 1088 Lig2 LIG C15 ARG 630 C 3.74 1088 Lig2LIG C17 ARG 630 CB 3.76 1088 Lig2 LIG C16 ARG 630 CB 3.82 1088 Lig2 LIGC11 ARG 630 CB 3.86 1088 Lig2 LIG C15 LEU 581 CD2 3.83 1088 Lig2 LIG C16LEU 575 CG 3.8 1088 Lig2 LIG N31 PHE 529 CE2 3.7 1088 Lig2 LIG C30 PHE529 CE2 3.48 1088 Lig2 LIG N29 PHE 529 CE2 3.88 1088 Lig2 LIG C24 PHE529 CE2 3.7 1088 Lig2 LIG C30 PHE 529 CZ 3.43 1088 Lig2 LIG N29 PHE 529CZ 3.47 1088 Lig2 LIG C28 PHE 529 CZ 3.55 1088 Lig2 LIG C27 PHE 529 CZ3.67 1088 Lig2 LIG C25 PHE 529 CZ 3.76 1088 Lig2 LIG C24 PHE 529 CZ 3.621088 Lig2 LIG N29 PHE 529 CE1 3.66 1088 Lig2 LIG C28 PHE 529 CE1 3.641088 Lig2 LIG C30 GLY 528 O 3.41 1088 Lig2 LIG N29 GLY 528 C 3.57 1088Lig2 LIG N29 GLY 528 CA 3.67 1088 Lig2 LIG C28 GLY 528 N 3.64 1088 Lig2LIG N29 ASP 526 C 3.64 1088 Lig2 LIG C28 ASP 526 C 3.67 1088 Lig1 LIGC16 GLY 579 O 3.7 1088 Lig1 LIG C15 GLY 579 O 3.61 1088 Lig1 LIG C16 LEU575 CD2 3.78 1088 Lig1 LIG C15 LEU 575 CD2 3.51 1088 Lig1 LIG C14 LEU575 CD2 3.86 1088 Lig1 LIG C30 GLU 487 OE2 3.58 1088 Lig1 LIG C30 GLU487 OE1 3.77 1088 Lig1 LIG C28 GLU 487 OE1 3.38 1088 Lig1 LIG N31 GLU487 CD 3.83 1088 Lig1 LIG N29 GLU 487 CD 3.32 1088 Lig1 LIG C28 THR 466CG2 3.77 1088 Lig1 LIG C27 THR 466 CG2 3.52 1088 Lig1 LIG C30 GLY 465 O3.59 1088 Lig1 LIG C24 GLY 465 O 3.68 1088 Lig1 LIG N31 GLY 465 CA 3.841065 MPD1 MPD C1 SER 633 OG 3.55 1065 MPD1 MPD CM SER 633 OG 3.61 1065MPD1 MPD C2 SER 633 OG 3.42 1065 MPD1 MPD O2 SER 633 CB 3.38 1065 MPD1MPD CM SER 633 CB 3.85 1065 MPD1 MPD O2 GLY 631 CA 3.69 1065 MPD1 MPD C4GLY 631 N 3.72 1065 MPD1 MPD O2 ARG 630 C 3.76 1065 MPD1 MPD C3 ARG 630NH1 3.58 1065 MPD1 MPD C3 ARG 630 CZ 3.66 1065 MPD1 MPD O2 ARG 630 CA3.71 1065 MPD1 MPD CM THR 467 O 3.89 1065 MPD1 MPD C5 THR 467 O 3 1065MPD1 MPD C4 THR 467 O 3.14 1065 MPD1 MPD C5 THR 467 C 3.67 1065 MPD1 MPDC5 THR 467 CB 3.88 1065 MPD1 MPD C5 THR 467 CA 3.74 1065 MPD1 MPD C5 THR467 N 3.17 1065 MPD1 MPD CM THR 466 CB 3.87 1065 MPD1 MPD C5 THR 466 CB3.72 1030 SO4_1 SO4 O1 MET 586 CE 3 1030 SO4_1 SO4 O1 ASN 584 CG 3.841030 SO4_1 SO4 O1 ASN 584 CB 3.5 1030 SO4_1 SO4 O1 ASN 584 CA 3.77 1030SO4_1 SO4 S ARG 583 NH1 3.88 1030 SO4_1 SO4 O2 ARG 583 CZ 3.79 1030SO4_1 SO4 O4 ARG 583 CZ 3.85 1030 SO4_1 SO4 O2 ARG 583 CD 3.83 1030SO4_1 SO4 O2 ARG 583 CG 3.5 1030 SO4_1 SO4 O2 ARG 583 CB 3.36 1030 SO4_1SO4 O2 ARG 583 CA 3.62 1030 SO4_1 SO4 S ARG 583 N 3.49 1030 SO4_1 SO4 O2ALA 582 C 3.71 1030 SO4_1 SO4 O1 ALA 582 CB 3.75 1030 SO4_1 SO4 O3 ALA582 CA 3.81 1030 SO4_1 SO4 O2 ALA 582 CA 3.73 1030 SO4_1 SO4 O1 ALA 582CA 3.88 1030 SO4_1 SO4 S ARG 578 NH2 3.7 1030 SO4_2 SO4 S SER 633 OG3.38 1030 SO4_2 SO4 O3 SER 633 CB 3.75 1030 SO4_2 SO4 O1 SER 633 CB 3.191030 SO4_2 SO4 O1 GLY 631 CA 3.8 1030 SO4_2 SO4 S GLY 631 N 3.86 1030SO4_2 SO4 O1 ARG 630 C 3.67 1030 SO4_2 SO4 O4 ARG 630 CZ 3.26 1030 SO4_2SO4 O4 ARG 630 CD 3.73 1030 SO4_2 SO4 O4 ARG 630 CB 3.69 1030 SO4_2 SO4O1 ARG 630 CA 3.56 1030 SO4_2 SO4 O3 HIS 483 CD2 3.13 1030 SO4_2 SO4 O3HIS 483 CE1 3.79 1030 PEG PEG O2 PRO 608 CD 3.6 1030 PEG PEG O2 TYR 607CD1 3.5 1030 PEG PEG C4 PHE 529 CD2 3.8 1030 PEG PEG C4 GLY 528 CA 3.771030 PEG PEG O4 GLY 528 CA 3 melagatran ACT ACT OXT ARG 646 CG 3.65melagatran ACT ACT OXT ARG 646 CB 3.44 melagatran ACT ACT OXT THR 644CG2 3.88 melagatran ACT ACT C THR 644 OG1 3.8 melagatran ACT ACT OXT THR644 CB 3.57 melagatran ACT ACT C ASP 641 OD2 3.45 melagatran ACT ACT CH3CYS 552 SG 3.79 melagatran ACT ACT CH3 CYS 552 CB 3.78 1090 GOL GOL C1SER 633 OG 3.59 1090 GOL GOL O1 SER 633 CB 3.17 1090 GOL GOL C2 GLY 631N 3.75 1090 GOL GOL C1 HIS 483 NE2 3.82 1090 GOL GOL O3 THR 466 CG2 3.881090 GOL GOL O2 THR 466 CB 3.75 1089 Lig2 LIG C23 GLU 487 OE2 3.61 1089Lig2 LIG C23 GLU 487 OE1 3.66 1089 Lig2 LIG C22 GLU 487 OE1 3.36 1089Lig2 LIG N5 GLU 487 CD 3.79 1089 Lig2 LIG N4 GLU 487 CD 3.36 1089 Lig2LIG C23 GLY 465 O 3.53 1089 Lig2 LIG C18 GLY 465 O 3.68 1097 PO4_1 PO4O3 SER 633 CB 3.34 1097 PO4_1 PO4 O1 SER 633 CB 3.64 1097 PO4_1 PO4 PSER 633 CB 3.73 1097 PO4_1 PO4 O4 SER 633 CB 3.51 1097 PO4_1 PO4 O3 GLY631 CA 3.63 1097 PO4_1 PO4 O3 ARG 630 C 3.78 1097 PO4_1 PO4 O3 ARG 630CG 3.89 1097 PO4_1 PO4 O2 ARG 630 CG 3.54 1097 PO4_1 PO4 O3 ARG 630 CA3.75 1097 PO4_1 PO4 O1 HIS 483 CD2 3.14 1097 PO4_1 PO4 O4 ALA 468 CB3.82 1097 PO4_1 PO4 O4 ALA 468 CA 3.86 1097 PO4_1 PO4 O4 THR 467 C 3.771097 PO4_2 PO4 O3 SER 633 CB 3.54 1097 PO4_2 PO4 O1 SER 633 CB 3.06 1097PO4_2 PO4 P SER 633 CB 3.63 1097 PO4_2 PO4 O4 SER 633 CB 3.64 1097 PO4_2PO4 O1 GLY 631 CA 3.73 1097 PO4_2 PO4 O1 ARG 630 C 3.82 1097 PO4_2 PO4O2 ARG 630 CG 3.6 1097 PO4_2 PO4 O1 ARG 630 CA 3.76 1097 PO4_2 PO4 O4HIS 483 CD2 3.22 1097 PO4_2 PO4 O3 ALA 468 CB 3.73 1097 PO4_2 PO4 O3 THR467 C 3.75 Abbreviations used: polyethylene glycol (PEG), succinic acid(SIN), sulfate (SO₄), glycerol (GOL), 2-methyl-2,4-pentanediol (MPD),phosphate (PO₄), acetic acid (ACT), surplus ligand (LIG) molecules.

Advantageously, after one or more binding sites has been identified asabove it is then possible to identify each of the amino acids thatparticipate in the binding. These specific amino acids interact with thecandidate molecules through hydrogen-bonding, ionic bonding and van derWaals interactions such as short-range electrostatic attractive forcesbetween uncharged molecules.

After a docking campaign has been performed, it is possible to analyzethe intermolecular interactions and prepare a rule set which describesthe interactions. The compound with MASP-2 inhibitory activity interactswith a MASP-2 binding site in an enzyme-inhibitor complex with aplurality of intermolecular interactions. In certain aspects, themolecule is described with complete specificity and description by thenumber and type(s) of intermolecular interactions within a MASP-2binding site, using an empirically derived rule set such as aninteraction rule set.

3. Rule Sets

In certain aspects, the compounds with MASP-2 inhibitory activityinteract with the MASP-2 binding site as an enzyme-inhibitor complex.The compound having MASP-2 inhibitory activity has between 1 and 100intermolecular interactions between itself and MASP-2 such as 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, 97, 98, 99, 100, or more intermolecular interactions with thebinding site of MASP-2. These intermolecular interactions types can be ahydrogen-bond, an ionic bond, an electrostatic bond, π-π interactions, avan der Waals interaction, binding of a water molecule or combinationsthereof. The numbers within the various types of intermolecularinteractions are counted to reach a total.

In certain aspects, a plurality of the same type of intermolecularinteractions exists. For example, the enzyme-inhibitor complex may have1-40 hydrogen-bonds, 1-40 ionic bonds, 1-40 electrostatic bonds, 1-40π-π interactions, 1-40 van der Waals interactions, 1-40 binding of watermolecules and combinations of thereof, wherein each of the foregoing1-40 range means 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35, 36, 37, 38, 39, 40, or more interactions. In certain aspects, aplurality or multiple intermolecular interactions may exist with thesame amino acid within the binding site.

In certain instances, an inhibitory molecule is described by a rule set.The compound with MASP-2 inhibitory activity interacts with the MASP-2binding site with a plurality of intermolecular interactions or rules.In certain aspects, the molecule is described with complete structuraland functional specificity and description by the number and type(s) ofintermolecular interactions. These rules have been empirically derivedand discovered using the methods herein.

In certain instances, the present disclosure provides a compound withMASP-2 inhibitory activity, wherein the compound interacts with abinding site, the interactions being one or more of (a) to (e):

-   -   a) the compound interacts via H-bonds with one or more amino        acid residues in the binding site of SEQ ID NO: 1;    -   b) the compound interacts via ionic or electrostatic        interactions or hydrogen bonding in the binding site of SEQ ID        NO: 1;    -   c) the compound interacts via a water molecule in a binding site        of SEQ ID NO: 1;    -   d) the compound interacts via π-π interactions with one or more        amino acid residues in the binding site of SEQ ID NO: 1; and/or    -   e) the compound interacts via van der Waals contacts to one or        more amino acid residues in the binding site of SEQ ID NO: 1,        wherein the compound is not an endogenous ligand.

In certain aspects, the compound has 1, 2, 3, 4, or 5 of theinteractions (a)-(e).

In addition to identifying virtual binding sites, it is also useful touse crystallographic data derived from a number of enzyme-inhibitorcomplex co-crystals to derive rule sets. In certain instances, thecrystallographic data from at least 1, 10, 20, 30, 40, 50, up to 100.For example, 30 co-crystals can be used 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, or 30 or even more enzyme-inhibitor complex crystals can be used togenerate a set of rules. Using the co-crystal structural data, it ispossible to describe the binding site and inhibitory compounds withinangstrom detail and definition. The following rule set was empiricallyderived using crystallographic data with a number of enzyme-inhibitorcomplex co-crystals.

In certain instances, an inhibitory molecule is described by a rule set.The compound with MASP-2 inhibitory activity interacts with the MASP-2serine protease domain in an enzyme-inhibitor complex with a pluralityof intermolecular interactions or rules. In certain aspects, themolecule is described with complete structural and functionalspecificity and description by the number and type(s) of intermolecularinteractions. These rules have been empirically derived and discoveredusing crystallographic data with a number of enzyme-inhibitor complexco-crystals. In certain instances, the crystallographic data from atleast 1, 10, 20, 30, 40, 50, up to 100. For example, 30 co-crystals canbe used 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or even moreenzyme-inhibitor complex crystals can be used to generate a set ofrules. Using the co-crystal structure information, it is possible todescribe the binding site and inhibitory compounds within angstromdetail and definition.

In certain instances, a plurality of amino acids within the MASP-2serine protease domain are involved in the intermolecular interactions.Amino acids within the MASP-2 serine protease domain include, but arenot limited to, ASP 627, SER 628, SER 654, GLY 656, GLN 665, SER 657,PHE 529, TYR 607, TRP 655, GLY 667, SER 633, ARG 630, CYS 629, HIS 483,PRO 606, PRO 608, SER 611, VAL 653, MET 658, TYR 669, ASN 659, CYS 660,GLN 665.

In certain aspects, the number of amino acids within the serine proteasedomain that interact with a compound having MASP-2 inhibitory activityor that make up a rule set is about 1-50, or 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, or 50 amino acids within the MASP-2 serine proteasedomain.

In certain instances, an inhibitor of the present disclosure is bound toMASP-2, rendering MASP-2 inactive. The amino acids of MASP-2 interactthrough intermolecular interactions with the inhibitor compound and thetypes of interactions are now described in more detail.

In certain aspects, the type of interactions include a hydrogen bond(H-bond). The enzyme-inhibitor complex may include 1-40 intermolecularH-bonds with one or more of the following 6 amino acids: ASP 627, SER628, SER 654, GLY 656, GLN 665 and SER 657. The 1-40 intermolecularH-bonds can include one or more atoms of the inhibitor with one or moreatoms of ASP 627, SER 628, SER 654, GLY 656, GLN 665 and SER 657. Eachamino acid can have more than one H-bond interaction with an inhibitor.In certain instances, the same atom can be hydrogen bonded to one ormore partners. In other words, a single atom of an inhibitory moleculecan interact with 2 or more atoms on the protein. In certain instances,there are 1-10H-bonds, or 2-8H-bonds, or 1, 2, 3, 4, 5, 6, 7, 8, 9, or10H-bonds per compounds.

In certain aspects, the type of interactions include an ionic and/or anelectrostatic interaction. The enzyme-inhibitor complex may include 1-10intermolecular ionic and/or electrostatic interactions with ASP 627. ASP627 can have more than one ionic and or electrostatic interaction withan inhibitor.

In certain other aspects, the type of interaction is binding of a watermolecule with ASP 627, GLN 665, SER 657, ASN 659, SER 628, GLU 662, ARG630, VAL 668, TYR 602, TYR 607. The enzyme-inhibitor complex may include1-30 bound water molecules 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 tovarious amino acids, other water molecules, to the compounds orcombinations thereof.

In certain other instances, the type of interaction includes one or more(e.g., a plurality or 1-40) π-π interactions with one or more of thefollowing amino acids PHE 529, TYR 607, and/or TRP 655, 1, 2 or 3 aminoacids. Each of the foregoing amino acids can have more than one π-πinteraction.

In certain aspects, the type of interaction also includes one or moresuch as 1-40, van der Waals interactions with GLY 667, SER 657, GLY 656,TRP 655, SER 654, SER 633, ARG 630, CYS 629, SER 628, ASP 627, PHE 529,HIS 483, PRO 606, TYR 607, PRO 608, SER 611, VAL 653, MET 658, TYR 669,ASN 659, CYS 660, GLN 665 and combinations thereof, which interactionsare specific MASP-2 amino acids within the serine protease domain ofMASP-2.

III. Synthesis

Compounds described herein, including salts thereof, can be preparedusing known organic synthesis techniques and can be synthesizedaccording to any of numerous possible synthetic routes, such as thoseillustrated in the Examples below.

The reactions for preparing compounds described herein can be carriedout in suitable solvents which can be readily selected by one of skillin the art of organic synthesis. Suitable solvents can be substantiallynon-reactive with the starting materials (reactants), the intermediatesor products at the temperatures at which the reactions are carried out,e.g., temperatures which can range from the solvent's freezingtemperature to the solvent's boiling temperature. A given reaction canbe carried out in one solvent or a mixture of more than one solvent.Depending on the particular reaction step, suitable solvents for aparticular reaction step can be selected by the skilled artisan.

Preparation of compounds of the invention can involve the protection anddeprotection of various chemical groups. The need for protection anddeprotection, and the selection of appropriate protecting groups, can bereadily determined by one skilled in the art. The chemistry ofprotecting groups is described, e.g., in Kocienski, Protecting Groups,(Thieme, 2007); Robertson, Protecting Group Chemistry, (OxfordUniversity Press, 2000); Smith et al., March's Advanced OrganicChemistry: Reactions, Mechanisms, and Structure, 6th Ed. (Wiley, 2007);Peturssion et al., “Protecting Groups in Carbohydrate Chemistry,” J.Chem. Educ., 1997, 74(11), 1297; and Wuts et al., Protective Groups inOrganic Synthesis, 4th Ed., (Wiley, 2006).

Reactions can be monitored according to any suitable method known in theart. For example, product formation can be monitored by spectroscopicmeans, such as nuclear magnetic resonance spectroscopy (e.g., ¹H or¹³C), infrared spectroscopy, spectrophotometry (e.g., UV-visible), massspectrometry or by chromatographic methods such as high performanceliquid chromatography (HPLC) or thin layer chromatography (TLC).

The particular synthetic methods used in the Examples provide generalguidance in connection with preparing the compounds of the invention.One skilled in the art would understand that the preparations can bemodified or optimized using general knowledge of organic chemistry toprepare various compounds within the scope of the present disclosure.

Starting materials, reagents and intermediates whose synthesis is notdescribed herein are either commercially available, known in theliterature, or may be prepared by methods known to one skilled in theart.

It will be appreciated by one skilled in the art that the processesdescribed are not the exclusive means by which compounds of theinvention may be synthesized and that a broad repertoire of syntheticorganic reactions is available to be potentially employed insynthesizing compounds of the invention. The person skilled in the artknows how to select and implement appropriate synthetic routes. Suitablesynthetic methods of starting materials, intermediates and products maybe identified by reference to the literature, including referencesources such as: Advances in Heterocyclic Chemistry, Vols. 1-107(Elsevier, 1963-2012); Journal of Heterocyclic Chemistry, Vols. 1-49(Journal of Heterocyclic Chemistry, 1964-2012); Carreira, et al. (Ed.)Science of Synthesis, Vols. 1-48 (2001-2010) and Knowledge UpdatesKU2010/1-4; 2011/1-4; 2012/1-2 (Thieme, 2001-2012); Katritzky, et al.(Ed.) Comprehensive Organic Functional Group Transformations, (PergamonPress, 1996); Katritzky et al. (Ed.); Comprehensive Organic FunctionalGroup Transformations II (Elsevier, 2nd Edition, 2004); Katritzky et al.(Ed.), Comprehensive Heterocyclic Chemistry (Pergamon Press, 1984);Katritzky et al., Comprehensive Heterocyclic Chemistry II (PergamonPress, 1996); Smith et al., March's Advanced Organic Chemistry:Reactions, Mechanisms, and Structure, 6th Ed. (Wiley, 2007); Trost etal. (Ed.), Comprehensive Organic Synthesis (Pergamon Press, 1991).

IV. Methods of Treatment

In another aspect, the present disclosure provides a method of treatinga patient suffering from, or at risk for developing a MASP-2-associateddisease or disorder such as a MASP-2-dependent complement-associateddisease or disorder comprising administering a small molecule inhibitorof MASP-2.

The compound can be any small molecule inhibitor of MASP-2. In someembodiments, the compound can be a small molecule inhibitor of MASP-2that binds to the serine protease domain of MASP-2. In some embodiments,the compound can be a small molecule inhibitor such as a synthetic smallmolecule inhibitor of MASP-2. In some embodiments, the compound can be asmall molecule inhibitor of MASP-2 that binds to the catalytic,substrate-binding region of MASP-2. In some embodiments, the compoundselectively inhibits MASP-2 as compared to thrombin. In someembodiments, the compound can be any small molecule inhibitor of MASP-2that binds to a binding site comprising the S1, S2 and S3 regions, andoptionally, further comprises the S4 and RM regions, of the MASP-2enzyme described herein. In some embodiments, the compound can be anysmall molecule that binds to a binding site of comprising the aminoacids ALA 468, ALA 469, HIS 483, ASP 526, ALA 527, GLY 528, PHE 529, LEU575, TYR 602, PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS629, ARG 630, GLY 631, ASP 632, SER 633, GLY 634, GLY 635, VAL 653, SER654, TRP 655, GLY 656, SER 657, MET 658, ASN 659, CYS 660, GLU 662, GLN665, TYR 666, GLY 667, VAL 668, and TYR 669, or any subset of any 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or 36 of the aminoacids ALA 468, ALA 469, HIS 483, ASP 526, ALA 527, GLY 528, PHE 529, LEU575, TYR 602, PRO 606, TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS629, ARG 630, GLY 631, ASP 632, SER 633, GLY 634, GLY 635, VAL 653, SER654, TRP 655, GLY 656, SER 657, MET 658, ASN 659, CYS 660, GLU 662, GLN665, TYR 666, GLY 667, VAL 668, and/or TYR 669.

The compound can be any small molecule inhibitor of MASP-2 as disclosedherein. In some embodiments, the compound can be any of the compoundsdisclosed above under “II. Compounds” above, or any embodiment thereof.

As described in U.S. Pat. Nos. 7,919,094; 8,840,893; 8,652,477;8,951,522, 9,011,860, 9,475,885, 9,644,035, U.S. Patent ApplicationPublication Nos. US2013/0344073, US2013/0266560, US 2015/0166675,US2017/0137537, US2017/0166660, US2017/0189525, US2017/0267781,US2017/0283508, US2017/0253667, US2018/0105604, WO2018/045054,WO2019/036460 and co-pending U.S. Patent Application Ser. No. 62/688,611(each of which is assigned to Omeros Corporation, the assignee of theinstant application, each of which is hereby incorporated by reference),MASP-2-dependent complement activation has been implicated ascontributing to the pathogenesis of numerous acute and chronic diseasestates. For example, as described in U.S. Pat. No. 8,951,522, theprimary function of the complement system, a part of the innate immunesystem, is to protect the host against infectious agents, however,inappropriate or over-activation of the complement system can lead toserious disease, such as thrombotic microangiopathies (TMAs, includingaHUS, TTP and HUS) in which endothelial damage as well as fibrin andplatelet-rich thrombi in the microvasculature lead to organ damage. Thelectin pathway plays a dominant role in activating complement insettings of endothelial cell stress or injury, and preventing theactivation of MASP-2 and the lectin pathway halts the sequence ofenzymatic reactions that lead to the formation of the membrane attackcomplex, platelet activation and leukocyte recruitment. As described inU.S. Pat. No. 8,652,477, in addition to initiation of the lectinpathway, MASP-2 can also activate the coagulation system and is capableof cleaving prothrombin to thrombin.

Accordingly, in some embodiments, the method comprises administering toa patient suffering from or at risk for developing a MASP-2-dependentcomplement-associated disease or disorder an amount of a compound of thedisclosure in an amount sufficient to inhibit MASP-2 dependentcomplement activation in said mammalian subject to thereby treat thedisease or disorder. In some embodiments, the method can furthercomprise, prior to administering a compound of the disclosure to thepatient, determining that the patient is afflicted with the lectincomplement-associated disease or disorder.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is selected from the group consisting of a thromboticmicroangiopathy (TMA), a renal condition, an inflammatory reactionresulting from tissue or organ transplantation, an ischemia reperfusioninjury, a complication associated with diabetes, a cardiovasculardisease or disorder, an inflammatory gastrointestinal disorder, apulmonary disorder, an ophthalmic disease or disorder, disseminatedintravascular coagulation, graft-versus-host disease, veno-occlusivedisease and diffuse alveolar hemorrhage.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a thrombotic microangiopathy (TMA) including thromboticthrombocytopenic purpura (TTP), refractory TTP, Upshaw-Schulman Syndrome(USS), hemolytic uremic syndrome (HUS), atypical hemolytic syndrome(aHUS), non-Factor H-dependent atypical hemolytic syndrome, aHUSsecondary to an infection, plasma therapy-resistant aHUS, a TMAsecondary to cancer, a TMA secondary to chemotherapy, a TMA secondary totransplantation, or a TMA associated with hematopoietic stem celltransplant.

In some embodiments, the method comprises administering to a patientsuffering from or at risk for developing graft-versus-host disease(GVHD), including acute GVHD, chronic GVHD or steroid-resistant GVHD anamount of a compound of the disclosure in an amount sufficient toinhibit MASP-2 dependent complement activation in said mammalian subjectto thereby treat the disease or disorder. In some embodiments, thesubject suffering from or at risk for developing GVHD has previouslyundergone, is undergoing, or will undergo a hematopoietic stem celltransplant.

In some embodiments, the method comprises administering to a patientsuffering from, or at risk for developing diffuse alveolar hemorrhage(DAH) an amount of a compound of the disclosure in an amount sufficientto inhibit MASP-2 dependent complement activation in said mammaliansubject to thereby treat the disease or disorder. In some embodiments,the subject suffering from, or at risk for developing DAH has previouslyundergone, is undergoing, or will undergo a hematopoietic stem celltransplant.

In some embodiments, the method comprises administering to a patientsuffering from, or at risk for developing veno-occlusive disease (VOD)an amount of a compound of the disclosure in an amount sufficient toinhibit MASP-2 dependent complement activation in said mammalian subjectto thereby treat the disease or disorder. In some embodiments, thesubject suffering from, or at risk for developing VOD has previouslyundergone, is undergoing, or will undergo a hematopoietic stem celltransplant.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a renal condition including, but not limited to,mesangioproliferative glomerulonephritis, membranous glomerulonephritis,membranoproliferative glomerulonephritis (mesangiocapillaryglomerulonephritis), acute post infectious glomerulonephritis(poststreptococcal glomerulonephritis), C3 glomerulopathy,cryoglobulinemic glomerulonephritis, pauci-immune necrotizing crescenticglomerulonephritis, lupus nephritis, Henoch-Schonlein purpura nephritisand IgA nephropathy.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is renal fibrosis (e.g., tubulointerstitial fibrosis) and/orproteinuria in a subject suffering from or at risk for developingchronic kidney disease, chronic renal failure, glomerular disease (e.g.,focal segmental glomerulosclerosis), an immune complex disorder (e.g.,IgA nephropathy, membranous nephropathy), lupus nephritis, nephroticsyndrome, diabetic nephropathy, tubulointerstitial damage andglomerulonepthritis (e.g., C3 glomerulopathy), or a disease or conditionassociated with proteinuria, including, but not limited to, nephroticsyndrome, pre-eclampsia, eclampsia, toxic lesions of kidneys,amyloidosis, collagen vascular diseases (e.g., systemic lupuserythematosus), dehydration, glomerular diseases (e.g., membranousglomerulonephritis, focal segmental glomerulonephritis, C3glomerulopathy, minimal change disease, lipoid nephrosis), strenuousexercise, stress, benign orthostatis (postural) proteinuria, focalsegmental glomerulosclerosis, IgA nephropathy (i.e., Berger's disease),IgM nephropathy, membranoproliferative glomerulonephritis, membranousnephropathy, minimal change disease, sarcoidosis, Alport's syndrome,diabetes mellitus (diabetic nephropathy), drug-induced toxicity (e.g.,NSAIDS, nicotine, penicillamine, lithium carbonate, gold and other heavymetals, ACE inhibitors, antibiotics (e.g., adriamycin) or opiates (e.g.,heroin) or other nephrotoxins); Fabry's disease, infections (e.g., HIV,syphilis, hepatitis A, B or C, poststreptococcal infection, urinaryschistosomiasis); aminoaciduria, Fanconi syndrome, hypertensivenephrosclerosis, interstitial nephritis, sickle cell disease,hemoglobinuria, multiple myeloma, myoglobinuria, organ rejection (e.g.,kidney transplant rejection), ebola hemorrhagic fever, Nail patellasyndrome, familial Mediterranean fever, HELLP syndrome, systemic lupuserythematosus, Wegener's granulomatosis, Rheumatoid arthritis, Glycogenstorage disease type 1, Goodpasture's syndrome, Henoch-Schonleinpurpura, urinary tract infection which has spread to the kidneys,Sjogren's syndrome and post-infections glomerulonepthritis.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an inflammatory reaction resulting from tissue or solidorgan transplantation including, but not limited to, allotransplantationor xenotransplantation of whole organs (e.g., kidney, heart, liver,pancreas, lung, cornea, and the like) or tissue grafts (e.g., valves,tendons, bone marrow, and the like).

In some embodiments, the MASP-2-dependent complement-associated disorderis an ischemia reperfusion injury (I/R), including but not limited to,myocardial I/R, gastrointestinal I/R, renal I/R, and I/R following anaortic aneurism repair, I/R associated with cardiopulmonary bypass,cerebral I/R, stroke, organ transplant or reattachment of severed ortraumatized limbs or digits; revascularization to transplants and/orreplants, and hemodynamic resuscitation following shock and/or surgicalprocedures.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a complication associated with non-obese diabetes (Type-1diabetes or Insulin-dependent diabetes mellitus) and/or complicationsassociated with Type-1 or Type-2 (adult onset) diabetes including, butnot limited to diabetic angiopathy, diabetic neuropathy, diabeticretinopathy or diabetic macular edema.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a cardiovascular disease or disorder, including but notlimited to, Henoch-Schonlein purpura nephritis, systemic lupuserythematosus-associated vasculitis, vasculitis associated withrheumatoid arthritis (also called malignant rheumatoid arthritis),immune complex vasculitis, and Takayasu's disease; dilatedcardiomyopathy; diabetic angiopathy; Kawasaki's disease (arteritis);venous gas embolus (VGE); and inhibition of restenosis following stentplacement, rotational atherectomy and/or percutaneous transluminalcoronary angioplasty (PTCA).

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an inflammatory gastrointestinal disorder, including butnot limited to, pancreatitis, diverticulitis and bowel disordersincluding Crohn's disease, ulcerative colitis, irritable bowel syndromeand inflammatory bowel disease (IBD).

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a pulmonary disorder, including but not limited to, acuterespiratory distress syndrome, transfusion-related acute lung injury,ischemia/reperfusion acute lung injury, chronic obstructive pulmonarydisease, asthma, Wegener's granulomatosis, antiglomerular basementmembrane disease (Goodpasture's disease), meconium aspiration syndrome,aspiration pneumonia, bronchiolitis obliterans syndrome, idiopathicpulmonary fibrosis, acute lung injury secondary to burn, non-cardiogenicpulmonary edema, transfusion-related respiratory depression andemphysema.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an extracorporeal exposure-triggered inflammatoryreaction and the method comprises treating a subject undergoing anextracorporeal circulation procedure including, but not limited to,hemodialysis, plasmapheresis, leukopheresis, extracorporeal membraneoxygenation (ECMO), heparin-induced extracorporeal membrane oxygenationLDL precipitation (HELP) and cardiopulmonary bypass (CPB).

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is selected from inflammatory or non-inflammatoryarthritides and other musculoskeletal disorders, including but notlimited to, osteoarthritis, rheumatoid arthritis, juvenile rheumatoidarthritis, gout, neuropathic arthropathy, psoriatic arthritis,ankylosing spondylitis or other spondyloarthropathies and crystallinearthropathies, muscular dystrophy and systemic lupus erythematosus(SLE).

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a skin disorder, including, but not limited to,psoriasis, autoimmune bullous dermatoses, eosinophilic spongiosis,bullous pemphigoid, epidermolysis bullosa acquisita, atopic dermatitis,herpes gestationis and other skin disorders, and for the treatment ofthermal and chemical burns including capillary leakage caused thereby.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a peripheral nervous system (PNS) and/or central nervoussystem (CNS) disorder or injury including, but not limited to, multiplesclerosis (MS), myasthenia gravis (MG), Huntington's disease (HD),amyotrophic lateral sclerosis (ALS), Guillain Barre syndrome,reperfusion following stroke, degenerative discs, cerebral trauma,Parkinson's disease (PD), Alzheimer's disease (AD), Miller-Fishersyndrome, cerebral trauma and/or hemorrhage, traumatic brain injury,demyelination and meningitis.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is sepsis or a condition resulting from sepsis includingwithout limitation severe sepsis, septic shock, acute respiratorydistress syndrome resulting from sepsis, hemolytic anemia, systemicinflammatory response syndrome, or hemorrhagic shock.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is a urogenital disorder including, but not limited to,painful bladder disease, sensory bladder disease, chronic abacterialcystitis and interstitial cystitis, male and female infertility,placental dysfunction and miscarriage and pre-eclampsia.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an inflammatory reaction in a subject being treated withchemotherapeutics and/or radiation therapy, including without limitationfor the treatment of cancerous conditions.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an angiogenesis-dependent cancer, including but notlimited to, a solid tumor(s), blood borne tumor(s), high-risk carcinoidtumors and tumor metastases.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an angiogenesis-dependent benign tumor, including but notlimited to, hemangiomas, acoustic neuromas, neurofibromas, trachomas,carcinoid tumors and pyogenic granulomas.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an endocrine disorder including, but not limited to,Hashimoto's thyroiditis, stress, anxiety and other potential hormonaldisorders involving regulated release of prolactin, growth orinsulin-like growth factor, and adrenocorticotropin from the pituitary.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an ophthalmic disease or disorder including, but notlimited to, age-related macular degeneration, glaucoma andendophthalmitis.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is an ocular angiogenic disease or condition including, butnot limited to age-related macular degeneration, uveitis, ocularmelanoma, corneal neovascularization, primary pterygium, HSV stromalkeratitis, HSV-1-induced corneal lymphangiogenesis, proliferativediabetic retinopathy, diabetic macular edema, retinopathy ofprematurity, retinal vein occlusion, corneal graft rejection,neovascular glaucoma, vitreous hemorrhage secondary to proliferativediabetic retinopathy, neuromyelitis optica and rubeosis.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is disseminated intravascular coagulation (DIC) or othercomplement mediated coagulation disorder, including DIC secondary tosepsis, severe trauma, including neurological trauma (e.g., acute headinjury, see Kumura et al, Acta Neurochirurgica 55:23-28 (1987),infection (bacterial, viral, fungal, parasitic), cancer, obstetricalcomplications, liver disease, severe toxic reaction {e.g., snake bite,insect bite, transfusion reaction), shock, heat stroke, transplantrejection, vascular aneurysm, hepatic failure, cancer treatment bychemotherapy or radiation therapy, burn, or accidental radiationexposure.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is selected from the group consisting of acute radiationsyndrome, dense deposit disease, Degos Disease, CatastrophicAntiphospholipid Syndrome (CAPS), Behcet's disease, cryoglobulinemia;paroxysmal nocturnal hemoglobinuria (“PNH”) and cold agglutinin disease.

In some embodiments, the MASP-2-dependent complement-associated diseaseor disorder is selected from the group consisting of aHUS, HSCT-TMA,IgAN, and Lupus Nepthritis (LN).

In some embodiments, the method comprises administering to a patientsuffering from, or at risk for developing a disease, disorder orcondition associated with fibrin-induced activation of the complementsystem and the associated activation of the coagulation and/or contactsystems an amount of a compound of the disclosure in an amountsufficient to inhibit MASP-2 dependent complement activation in saidmammalian subject to thereby treat the disease or disorder. In someembodiments, the subject is suffering from, or at risk of developing, adisease, disorder or condition associated with complement-relatedinflammation, excessive coagulation or contact system activationinitiated by fibrin or activated platelets. In some embodiments, thesubject is suffering from a disease or disorder selected from the groupconsisting of arterial thrombosis, venous thrombosis, deep veinthrombosis, post-surgical thrombosis, restenosis following coronaryartery bypass graft and/or an interventional cardiovascular procedure(e.g., angioplasty or stent placement), atherosclerosis, plaque rupture,plaque instability, restenosis, hypotension, acute respiratory distresssyndrome (ARDS), systemic inflammatory response syndrome (SIRS),disseminated intravascular coagulation (DIC), veno-occlusive disease(VOD), thrombotic microangiopathy, lupus nephritis, superficialthrombophlebitis, Factor V Leiden mutation, ischemic/reperfusion injury,human immunodeficiency virus (HIV) infection, undergoinghormone-replacement therapy (HRT), Alzheimer's disease and/or sufferingfrom a hypercoagulable state. In some embodiments, the subject issuffering from, or at risk for developing an acquired hypercoagulablestate due to at least one or more of the following: undergoing therapywith a drug selected from the group consisting of 5-FU, GM-CSF,cisplatin, heparin, COX-2 inhibitor, contrast media, corticosteroids andantipsychotics; venous stasis (immobilization, surgery, etc.),antiphospholipid syndrome, cancer (promyelocytic leukemia, lung, breast,prostate, pancreas, stomach and colon tumors), tissue injury due totrauma or surgery, presence of a catheter in a central vein, acquireddeficiency of a protein involved in clot formation (e.g., protein C),paroxysmal nocturnal hemoglobinuria (PNH), elevated levels ofhomocysteine, heart failure, presence of a mechanical valve, pulmonaryhypertension with in-situ thrombosis, atrial fibrillation,heparin-induced thrombocytopenia (HIT), heparin-induced thrombocytopeniaand thrombosis (HITT), Kawasaki disease with in-situ thrombus, Takayasuarteritis with in-situ thrombus, thrombophilia of metastatic cancer,elevated Factor VIII levels, pregnancy, inflammatory bowel disease(IBD), or due to a genetic defect that causes or increases the risk ofdeveloping, a hypercoagulable state, such as a genetic defect selectedfrom the group consisting of a Prothrombin 20210 gene mutation, an MTHFRmutation, a deficiency of protein C, a deficiency of protein S, adeficiency of protein A, a deficiency of protein Z, an antithrombindeficiency and a genetic disorder producing thrombophilia. In someembodiments, the subject is suffering from, or at risk for developing, adisease or disorder that is amenable to treatment with a kallikreininhibitor. In some embodiments, the subject is suffering from, or atrisk for developing a disease or disorder amenable to treatment with akallikrein inhibitor is selected from the group consisting of hereditaryangioedema, diabetic macular edema and bleeding during cardiopulmonarybypass. In some embodiments, the subject is suffering from, or at riskfor developing, a disease or disorder that is amenable to treatment witha thrombin inhibitor, such as arterial thrombosis, venous thrombosis,pulmonary embolism, atrial fibrillation, heparin-inducedthrombocytopenia, conversion from one anticoagulant to another, oroff-label use for extracorporeal circuit patency of continuous renalreplacement therapy (CRRT) in critically ill patients with HIT(maintenance). In some embodiments, the subject has previouslyexperienced, is currently suffering from, or is at risk for developingatrial fibrillation and the MASP-2 inhibitory compound is administeredin an amount sufficient to reduce the risk of stroke in said subject. Insome embodiments, the subject is suffering from, or at risk fordeveloping, a disease or disorder that is amenable to treatment with afactor XII inhibitor, such as deep vein thrombosis (both primaryprophylaxis and extended therapy), pulmonary embolism, nonvalvularatrial fibrillation, prevention of recurrent ischemia after acutecoronary syndrome in subjects with or without atrial fibrillation,end-stage renal disease, cerebral ischemia, angina, or to reduce orprevent clotting associated with medical devices (e.g., valves, smallcaliber grafts, etc.) and/or extracorporeal circuits. In someembodiments, the subject has previously experienced, is currentlysuffering from, or is at risk for developing nonvalvular atrialfibrillation and the MASP-2 inhibitory compound is administered in anamount sufficient to reduce the risk of stroke and/or embolism in saidsubject. In some embodiments, the subject has an acquired disease ordisorder that increases the propensity for thromboembolism, such as adisease or disorder selected from the group consisting ofatherosclerosis, antiphospholipid antibodies, cancer (e.g.,promyelocytic leukemia, lung, breast, prostate, pancreatic, stomach andcolon), hyperhomocysteinemia, infection, tissue injury, venous stasis(such as due to surgery, orthopedic or paralytic immobilization, heartfailure, pregnancy, or obesity) and a subject taking oral contraceptivesthat contain estrogen. In some embodiments, the subject is in need ofanticoagulant therapy and the MASP-2 inhibitory compound is used as areplacement for standard anticoagulant therapy (e.g., Warfarin). In someembodiments, the subject has a condition that normally prohibitsstandard anticoagulant therapy, such as CNS amyloid angiopathy. In someembodiments of the method, the MASP-2 inhibitory compound isadministered as a bridging agent perioperatively in a subject otherwiseon standard anticoagulation therapy. In some embodiments, the subjecthas sickle cell disease which is a vaso-occlusive disorder involvingactivation of platelets.

Atypical Hemolytic Uremic Syndrome (aHUS).

Atypical hemolytic uremic syndrome (aHUS) is part of a group ofconditions termed “Thrombotic microangiopathies.” In the atypical formof HUS (aHUS), the disease is associated with defective complementregulation and can be either sporadic or familial. Familial cases ofaHUS are associated with mutations in genes coding for complementactivation or complement regulatory proteins, including complementfactor H, factor I, factor B, membrane cofactor CD46 as well ascomplement factor H-related protein 1 (CFHR1) and complement factorH-related protein 3 (CFHR3). (Zipfel, P. F., et al., PloS Genetics3(3):e41 (2007)). The unifying feature of this diverse array of geneticmutations associated with aHUS is a predisposition to enhancedcomplement activation on cellular or tissue surfaces. A subject is arisk for developing aHUS upon the onset of at least one or more symptomsindicative of aHUS (e.g., the presence of anemia, thrombocytopeniaand/or renal insufficiency) and/or the presence of thromboticmicroangiopathy in a biopsy obtained from the subject. The determinationof whether a subject is at risk for developing aHUS comprisesdetermining whether the subject has a genetic predisposition todeveloping aHUS, which may be carried out by assessing geneticinformation (e.g. from a database containing the genotype of thesubject), or performing at least one genetic screening test on thesubject to determine the presence or absence of a genetic markerassociated with aHUS (i.e., determining the presence or absence of agenetic mutation associated with aHUS in the genes encoding complementfactor H (CFH), factor I (CFI), factor B (CFB), membrane cofactor CD46,C3, complement factor H-related protein 1 (CFHR1), or THBD (encoding theanticoagulant protein thrombodulin) or complement factor H-relatedprotein 3 (CFHR3), or complement factor H-related protein 4 (CFHR4))either via genome sequencing or gene-specific analysis (e.g., PCRanalysis), and/or determining whether the subject has a family historyof aHUS. Methods of genetic screening for the presence or absence of agenetic mutation associated with aHUS are well established, for example,see Noris M et al. “Atypical Hemolytic-Uremic Syndrome,” 2007 Nov. 16[Updated 2011 Mar. 10]. In: Pagon R A, Bird T D, Dolan C R, et al.,editors. GeneReviews™, Seattle (Wash.): University of Washington,Seattle.

Hematopoietic Stem Cell Transplant-Associated TMA (HSCT-TMA)

Hematopoietic stem cell transplant-associated TMA (HSCT-TMA) is alife-threatening complication that is triggered by endothelial injury.The kidney is the most commonly affected organ, though HSCT-TMA can be amulti-system disease that also involves the lung, bowel, heart andbrain. The occurrence of even mild TMA is associated with long-termrenal impairment. Development of post-allogeneic HSCT-associated TMAdiffers in frequency based on varying diagnostic criteria andconditioning and graft-versus-host disease prophylaxis regimens, withcalcineurin inhibitors being the most frequent drugs implicated (Ho V Tet al., Biol Blood Marrow Transplant, 11(8):571-5, 2005).

Immunoglobulin A Nephropathy (IgAN)

Immunoglobulin A nephropathy (IgAN) is an autoimmune kidney diseaseresulting in intrarenal inflammation and kidney injury. IgAN is the mostcommon primary glomerular disease globally. With an annual incidence ofapproximately 2.5 per 100,000, it is estimated that 1 in 1400 persons inthe U.S. will develop IgAN. As many as 40% of patients with IgAN willdevelop end-stage renal disease (ESRD). Patients typically present withmicroscopic hematuria with mild to moderate proteinuria and variablelevels of renal insufficiency (Wyatt R. J., et al., NEnglJ Med36S(25):2402-4, 2013). Clinical markers such as impaired kidneyfunction, sustained hypertension, and heavy proteinuria (over 1 g perday) are associated with poor prognosis (Goto M et al., Nephrol DialTransplant 24(10):3068-74, 2009; Berthoux F. et al., J Am Soc Nephrol22(4):752-61, 2011). Proteinuria is the strongest prognostic factorindependent of other risk factors in multiple large observationalstudies and prospective trials (Coppo R. et al., J Nephrol 18(5):503-12,2005; Reich H. N., et al., J Am Soc Nephrol 18(12):3177-83, 2007). It isestimated that 15-20% of patients reach ESRD within 10 years of diseaseonset if left untreated (D'Amico G., Am J Kidney Dis 36(2):227-37,2000). The diagnostic hallmark of IgAN is the predominance of IgAdeposits, alone or with IgG, IgM, or both, in the glomerular mesangium.

Lupus Nephritis (LN)

A main complication of systemic lupus erythematosus (SLE) is nephritis,also known as lupus nephritis, which is classified as a secondary formof glomerulonephritis. Up to 60% of adults with SLE have some form ofkidney involvement later in the course of the disease (Koda-Kimble etal., Koda-Kimble and Young's Applied Therapeutics: the clinical use ofdrugs, 10th Ed, Lippincott Williams & Wilkins: pages 792-9, 2012) with aprevalence of 20-70 per 100,000 people in the US. Lupus nephritis oftenpresents in patients with other symptoms of active SLE, includingfatigue, fever, rash, arthritis, serositis, or central nervous systemdisease (Pisetsky D. S. et al., Med Clin North Am 81(1): 113-28, 1997).Some patients have asymptomatic lupus nephritis; however, during regularfollow-up, laboratory abnormalities such as elevated serum creatininelevels, low albumin levels, or urinary protein or sediment suggestactive lupus nephritis.

V. Compositions, Dosage and Administration

The compounds as described herein can be administered in a mannercompatible with the dosage formulation, and in such amount as will beeffective or suitable for treatment. The quantity to be administereddepends on a variety of factors including, e.g., the age, body weight,physical activity, and diet of the individual, and the desired effect.In certain embodiments, the size of the dose may also be determined bythe existence, nature, and extent of any adverse side effects thataccompany the administration of the compound in a particular individual.

It will be understood, however, that the specific dose level andfrequency of dosage for any particular patient may be varied by aphysician and will depend upon a variety of factors including theactivity of the specific compound employed, the metabolic stability andlength of action of that compound, the age, body weight, hereditarycharacteristics, general health, sex, diet, mode and time ofadministration, rate of excretion, drug combination, the severity of theparticular condition, and the host undergoing therapy.

In certain embodiments, the dose may take the form of solid, semi-solid,or liquid forms, preferably in unit dosage forms suitable for simpleadministration of precise dosages.

As used herein, the term “unit dosage form” refers to physicallydiscrete units suitable as unitary dosages for humans and other mammals,each unit containing a predetermined quantity of an active agentcalculated to produce the desired onset, tolerability, and/orefficacious effects, in association with a suitable pharmaceuticalexcipient (e.g., an ampoule). In addition, more concentrated dosageforms may be prepared, from which the more dilute unit dosage forms maythen be produced.

The compounds described herein can be administered to a subject in needof treatment using methods known in the art, such as by oraladministration or by injection. The injection can be subcutaneous,intravenous, intraperitoneal, intramuscular. As described herein,parenteral formulations can be prepared in dosage unit form for ease ofadministration and uniformity of dosage. As used herein the term “unitdosage form” refers to physically discrete units suited as unitarydosages for the subject to be treated; each unit containing apredetermined quantity of active compound calculated to produce thedesired therapeutic effect.

The pharmaceutical compositions of the present application comprise atherapeutically effective amount of a compound of the presentapplication formulated together with one or more pharmaceuticallyacceptable carriers or excipient. As used herein, the term“pharmaceutically acceptable carrier” means a non-toxic, inert solid,semi-solid or liquid filler, diluent, encapsulating material orformulation auxiliary of any type. The pharmaceutical compositions ofthis application can be administered to humans and other animals orally,rectally, parenterally, intracistemally, intravaginally,intraperitoneally, topically (as by powders, ointments, or drops),buccally, or as an oral or nasal spray.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups andelixirs. In addition to the active compounds, the liquid dosage formsmay contain inert diluents commonly used in the art such as, forexample, water or other solvents, solubilizing agents and emulsifierssuch as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethylacetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butyleneglycol, dimethylformamide, oils (in particular, cottonseed, groundnut,corn, germ, olive, castor, and sesame oils), glycerol,tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid estersof sorbitan, and mixtures thereof. Besides inert diluents, the oralcompositions can also include adjuvants such as wetting agents,emulsifying and suspending agents, sweetening, flavoring, and perfumingagents.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions may be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation may also be a sterile injectablesolution, suspension or emulsion in a nontoxic parenterally acceptablediluent or solvent. Among the acceptable vehicles and solvents that maybe employed are water, Ringer's solution, U.S.P. and isotonic sodiumchloride solution. In addition, sterile, fixed oils are conventionallyemployed as a solvent or suspending medium. For this purpose, any blandfixed oil can be employed including synthetic mono- or diglycerides. Inaddition, fatty acids such as oleic acid are used in the preparation ofinjectables.

In order to prolong the effect of a drug, it is often desirable to slowthe absorption of the drug from subcutaneous or intramuscular injection.This may be accomplished by the use of a liquid suspension ofcrystalline or amorphous material with poor water solubility. The rateof absorption of the drug then depends upon its rate of dissolutionwhich, in turn, may depend upon crystal size and crystalline form.Alternatively, delayed absorption of a parenterally administered drugform is accomplished by dissolving or suspending the drug in an oilvehicle.

Solid compositions of a similar type may also be employed as fillers insoft and hard filled gelatin capsules using such excipients as lactoseor milk sugar as well as high molecular weight polyethylene glycols andthe like.

The active compounds can also be in micro-encapsulated form with one ormore excipients as noted above. The solid dosage forms of tablets,dragees, capsules, pills, and granules can be prepared with coatings andshells such as enteric coatings, release controlling coatings and othercoatings well known in the pharmaceutical formulating art. In such soliddosage forms the active compound may be admixed with at least one inertdiluent such as sucrose, lactose or starch. Such dosage forms may alsocomprise, as is normal practice, additional substances other than inertdiluents, e.g., tableting lubricants and other tableting aids such amagnesium stearate and microcrystalline cellulose. In the case ofcapsules, tablets and pills, the dosage forms may also comprisebuffering agents.

Dosage forms for topical or transdermal administration of a compound ofthis application include ointments, pastes, creams, lotions, gels,powders, solutions, sprays, inhalants or patches. The active componentis admixed under sterile conditions with a pharmaceutically acceptablecarrier or excipient and any needed preservatives or buffers as may berequired.

Transdermal patches have the added advantage of providing controlleddelivery of a compound to the body. Such dosage forms can be made bydissolving or dispensing the compound in the proper medium. Absorptionenhancers can also be used to increase the flux of the compound acrossthe skin. The rate can be controlled by either providing a ratecontrolling membrane or by dispersing the compound in a polymer matrixor gel.

According to the methods of treatment of the present application,disorders are treated or prevented in a subject, such as a human orother animal, by administering to the subject a therapeuticallyeffective amount of a compound of the application, in such amounts andfor such time as is necessary to achieve the desired result. The term“therapeutically effective amount” of a compound of the application, asused herein, means a sufficient amount of the compound so as to decreasethe symptoms of a disorder in a subject. As is well understood in themedical arts a therapeutically effective amount of a compound of thisapplication will be at a reasonable benefit/risk ratio applicable to anymedical treatment.

In general, compounds of the application will be administered intherapeutically effective amounts via any of the usual and acceptablemodes known in the art, either singly or in combination with one or moretherapeutic agents. A therapeutically effective amount may vary widelydepending on the severity of the disease, the age and relative health ofthe subject, the potency of the compound used and other factors.

In general, satisfactory results are indicated to be obtainedsystemically at daily dosages of from about 0.03 to 2.5 mg/kg per bodyweight. An indicated daily dosage in the larger mammal, e.g., humans, isin the range from about 0.5 mg to about 250 mg, about 5 mg to about 150mg, about 5 mg to about 100 mg, about 10 mg to about 75 mg, about 10 mgto about 50 mg, such as 10, 20, 30, 40, or about 50 mg, convenientlyadministered, e.g., in divided doses up to four times a day or in retardform. Suitable unit dosage forms for oral administration comprise fromca. 1 to 60 mg active ingredient.

In certain embodiments, a therapeutic amount or dose of the compounds ofthe present application may range from about 0.1 mg/kg to about 500mg/kg, alternatively from about 1 to about 50 mg/kg. In general,treatment regimens according to the present application compriseadministration to a patient in need of such treatment from about 10 mgto about 1000 mg of the compound(s) of this application per day insingle or multiple doses. Therapeutic amounts or doses will also varydepending on route of administration, as well as the possibility ofco-usage with other agents.

Upon improvement of a subject's condition, a maintenance dose of acompound, composition or combination of this application may beadministered, if necessary. Subsequently, the dosage or frequency ofadministration, or both, may be reduced, as a function of the symptoms,to a level at which the improved condition is retained when the symptomshave been alleviated to the desired level, treatment should cease. Thesubject may, however, require intermittent treatment on a long-termbasis upon any recurrence of disease symptoms.

It will be understood, however, that the total daily usage of thecompounds and compositions of the present application will be decided bythe attending physician within the scope of sound medical judgment. Thespecific inhibitory dose for any particular patient will depend upon avariety of factors including the disorder being treated and the severityof the disorder; the activity of the specific compound employed; thespecific composition employed; the age, body weight, general health, sexand diet of the patient; the time of administration, route ofadministration, and rate of excretion of the specific compound employed;the duration of the treatment; drugs used in combination or coincidentalwith the specific compound employed; and like factors well known in themedical arts.

The application also provides for a pharmaceutical combinations, e.g., akit, comprising a) a first agent which is a compound of the applicationas disclosed herein, in free form or in pharmaceutically acceptable saltform, and b) at least one co-agent. The kit can comprise instructionsfor its administration.

Methods for preparing such dosage forms are known to those skilled inthe art (see, e.g., REMINGTON'S PHARMACEUTICAL SCIENCES, 18th ED., MackPublishing Co., Easton, Pa. (1990)). The dosage forms typically includea conventional pharmaceutical carrier or excipient and may additionallyinclude other medicinal agents, carriers, adjuvants, diluents, tissuepermeation enhancers, solubilizers, and the like. Appropriate excipientscan be tailored to the particular dosage form and route ofadministration by methods well known in the art (see, e.g., REMINGTON'SPHARMACEUTICAL SCIENCES, 18th ED., Mack Publishing Co., Easton, Pa.(1990)).

EXAMPLES

The following examples are provided by way of illustration only and notby way of limitation. Those of skill will readily recognize a variety ofnoncritical parameters which could be changed or modified to yieldessentially similar results.

General Methods

If not otherwise stated, chromatography refers to flash chromatographyconducted on silica gel.

HPLC purification was performed by one of two methods. Method 1: on aGilson preparative reverse phase HPLC system with the combination ofUV/ELS detectors (254 nm and 280 nm) and ThermoFisher Hypersil GOLDAgilent (21.2×250 mm) 5 μm C-18 column. Eluents were a mixture of waterand acetonitrile (with 0.05% trifluoroacetic acid). Flow rate wastypically 20 mL/min with a linear gradient of water in acetonitrile from2-90% in 45 minutes. The injection volume was from 1 to 3 mL withmaximum 20 mg per load. Method 2: on a Waters preparative reverse phaseHPLC system with the combination of UV/MS detectors (254 nm and 280 nm)and XBridge Prep (19×50 mm) C18 10 μM OBD column. Eluents were a mixtureof water and acetonitrile (with 0.05% trifluoroacetic acid). Flow ratewas typically 50 mL/min with a linear gradient of water in acetonitrilefrom 5-95% in 8 minutes. The injection volume was from 0.2 to 1 mL withmaximum 20 mg per load.

Example 1: Preparation of((R)-2-((S)-2-((4-Carbamindoylbenzyl(carbamoyl)azetidin-1-ylcyclopropyl-2-oxoethyl)glycine(1028)

Step 1: To a stirred solution of Boc-D-cyclopropyl glycine (300 mg, 1.4mmol), methyl (S)-azetidine-2-carboxylate hydrochloride (211 mg, 1.4mmol) and DMAP (255 mg, 2.4 mmol) in MeCN (5 mL) at 5° C. was added EDC(293 mg, 1.5 mmol). The mixture was stirred for 48 h, then concentratedunder vacuum. The residue was dissolved in EtOAc and washed with H₂O,0.5 M KHSO₄ twice, saturated aqueous NaHCO₃, H₂O and brine, then dried(Na₂SO₄) and concentrated under vacuum. Chromatography (EtOAc-hexanes)gave methyl(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclopropylacetyl)azetidine-2-carboxylate(381 mg, 88% yield).

Step 2: To a solution of methyl(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclopropylacetyl)azetidine-2-carboxylate(381 mg) in THF (6 mL) was added 5 equiv of LiOH. The mixture wasstirred for 16 h at room temperature, then diluted with EtOAc, andadjusted to pH 3 with the slow addition of 10% KHSO₄. The mixture wassaturated with NaCl, and the layers were separated. The aqueous layerwas extracted with EtOAc (3×10 mL) and the combined organics were dried(Na₂SO₄) and concentrated under vacuum to give(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclopropylacetyl)azetidine-2-carboxylicacid as a solid foam that was used without further purification (380 mgcrude).

Step 3:(S)-1-((R)-2-((tert-Butoxycarbonyl)amino)-2-cyclopropylacetyl)azetidine-2-carboxylicacid was coupled with benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate following compound 1028,step 1. Chromatography (EtOAc-hexanes) gave tert-butyl((R)-2-((S)-2-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)carbamoyl)azetidin-1-yl)-1-cyclopropyl-2-oxoethyl)carbamateas a white foam (180 mg).

Step 4: A solution of tert-butyl((R)-2-((S)-2-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)carbamoyl)azetidin-1-yl)-1-cyclopropyl-2-oxoethyl)carbamate(180 mg) in EtOAc was cooled in an ice bath. Hydrogen chloride wasbubbled through the solution for approximately 5 min. The mixture wasallowed to reach room temp and stirred for 30 min. Et₂O was added to thesolution upon which a ppt formed. After the mixture was left at roomtemp for 16 h, the product was isolated by filtration, washed with Et₂Oand dried under vacuum. The resulting solid was dissolved in H₂O, madealkaline with 2 M NaOH and extracted with CH₂Cl₂ (3×10 mL). The combinedorganics were washed with brine, dried over Na₂SO₄ and concentratedunder vacuum to give benzyl((4-(((S)-1-((R)-2-amino-2-cyclopropylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamateas a white foam (115 mg, 78% yield over two steps).

Step 5: To a solution of benzyl((4-(((S)-1-((R)-2-amino-2-cyclopropylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamate(103 mg, 0.22 mmol) in MeCN (10 mL) was added bromobenzyl acetate (39μL, 0.245 mmol) and K₂CO₃ (77 mg, 0.556 mmol). The mixture was heated to60° C. and stirred for 16 h. The mixture was concentrated under vacuumand the residue was dissolved in EtOAc, washed with H₂O, dried overNa₂SO₄ and concentrated under vacuum. Chromatography (100% EtOAc then0-10% MeOH—CH₂Cl₂) gave benzyl((R)-2-((S)-2-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)carbamoyl)azetidin-1-yl)-1-cyclopropyl-2-oxoethyl)glycinate(20 mg, 15% yield).

Step 6: To a degassed solution of benzyl((R)-2-((S)-2-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)carbamoyl)azetidin-1-yl)-1-cyclopropyl-2-oxoethyl)glycinate(20 mg, 0.033 mmol) in EtOH was added 10% Pd/C (˜2 mg). The mixture wasstirred under 1 atm H₂ for 24 h. The mixture was filtered (0.2 μMsyringe filter) and the filtrate was concentrated under vacuum to give((R)-2-((S)-2-((4-carbamimidoylbenzyl)carbamoyl)azetidin-1-yl)-1-cyclopropyl-2-oxoethyl)glycine(12 mg).

Example 2: Preparation of(S)-1-((R)-2-Amino-2-cyclopropylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(1002)

Benzyl((4-(((S)-1-((R)-2-amino-2-cyclopropylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamatewas hydrogenated according to the method for compound 1028, step 6 toprovide(S)-1-((R)-2-amino-2-cyclopropylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide.

Example 3: Preparation of(S)-1-((R)-2-((2-amino-2-oxoethyl)amino)-2-cyclohexylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(1102)

Step 1: Benzyl((4-(((S)-1-((R)-2-amino-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the foregoing procedures with theappropriate starting materials. Reaction of benzyl((4-(((S)-1-((R)-2-amino-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamatewith bromoacetamide (1.2 equiv) and K₂CO₃ (2.5 equiv) according to theprocedure for compound 1028, step 5 gave benzyl((4-(((S)-1-((R)-2-((2-amino-2-oxoethyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamate(76% yield).

Step 2: Deprotection of benzyl((4-(((S)-1-((R)-2-((2-amino-2-oxoethyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamateaccording to compound 1028, step 6 provided(S)-1-((R)-2-((2-amino-2-oxoethyl)amino)-2-cyclohexylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(83% yield).

Example 4: Preparation of(S)-1-((R)-2-Acetamido-2-cyclohexylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(1154)

Step 1: To a solution of benzyl((4-(((S)-1-((R)-2-amino-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamate(170 mg, 0.337 mmol) in anhydrous CH₂Cl₂ (5 mL) at was added Et₃N (138μL, 1.0 mmol), acetic anhydride (41 μL, 0.405 mmol) and DMAP (2 mg). Themixture was stirred at room temp overnight then concentrated undervacuum. The residue was dissolved in EtOAc, washed with H₂O and dried(Na₂SO₄). Chromatography (100% EtOAc then 0-10% MeOH—CH₂Cl₂) gave benzyl((4-(((S)-1-((R)-2-acetamido-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamate(125 mg, 68% yield).

Step 2: Deprotection of benzyl((4-(((S)-1-((R)-2-acetamido-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)phenyl)(imino)methyl)carbamateaccording to compound 1028, step 6 provided(S)-1-((R)-2-acetamido-2-cyclohexylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(70 mg, 74% yield).

Example 5: Preparation of((R)-1-((S)-2-((4-Carbamimidoylbenzyl)carbamoyl)azetidin-1-yl)-1-oxopropan-2-yl)glycine(1009)

((R)-1-((S)-2-((4-Carbamimidoylbenzyl)carbamoyl)azetidin-1-yl)-1-oxopropan-2-yl)glycine was synthesized according to the method for compound 1028,except that Boc deprotection was performed in MeOH instead of EtOAc.

Example 6: Preparation of(S)-1-((R)-2-Amino-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(1058)

(S)-1-((R)-2-Amino-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamidewas synthesized according to the method for compound 1028 except thatmethyl ester hydrolysis was conducted with 1.5 equiv of LiOH in 1:1THF-H₂O.

Example 7: Preparation of(S)-1-((R)-2-amino-2-phenylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide(1011)

A solution of methyl (S)-azetidine-2-carboxylate (100 mg, 0.66 mmol),(R)-2-((tert-butoxycarbonyl)amino)-2-phenylacetic acid (150 mg, 0.60mmol), pyridine (0.16 mL) and EtOAc (0.33 mL) were cooled at −20 to −10°C. A solution of propylphosphonic anhydride in EtOAc (50% solution, 0.84mL) was added dropwise at a rate to maintain the internal temperaturebelow 0° C. The yellow solution was stirred at 0° C. for 18 h, thencooled to −10° C. and 1 M HCl (˜1 mL) was added dropwise. The reactionwas stirred at room temp for 2 h. EtOAc was added, the aqueous layerseparated and dried over Na₂SO₄. Concentration under vacuum followed bychromatography (50% EtOAc-hexanes) gave methyl(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-phenylacetyl)azetidine-2-carboxylate(80 mg). The remaining steps for the synthesis of compound 1011,(S)-1-((R)-2-amino-2-phenylacetyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide,were conducted according to the procedures for compound 1058.

Example 8: Preparation of(S)-1-(D-Prolyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide (1156)

(S)-1-(D-prolyl)-N-(4-carbamimidoylbenzyl)azetidine-2-carboxamide wassynthesized according to the procedures for compound 1058, except thatmethyl ester hydrolysis was conducted with 1.1 equiv LiOH and Bocremoval was conducted with TFA-CH₂Cl₂ (0.2 M) at 0° C. to room temp.

Example 9: Preparation of((R)-2-((S)-2-((4-Carbamimidoyl-3-hydroxybenzyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)glycine(1116)

Step 1: to an ice-cold solution of(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxylicacid (260 mg, 0.76 mmol) and DIEA (0.42 mL, 2.4 mmol) in anhyd MeCN (15mL) was added EDC (166 mg, 0.87 mmol) and HOBt (112 mg, 0.83 mmol). Themixture was stirred for 5 min then6-(aminomethyl)benzo[d]isoxazol-3-amine hydrochloride (183 mg, 0.92mmol, prepared according to WO 2001079195) was added. The mixture wasstirred for 18 h, allowed to warm to room temp, then concentrated undervacuum. The residue was dissolved in EtOAc, washed with H₂O and brine,dried over Na₂SO₄ and chromatographed with 65-100% EtOAc-hexanes to give305 mg of tert-butyl((R)-2-((S)-2-(((3-aminobenzo[d]isoxazol-6-yl)methyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)carbamate.

Step 2: Boc removal was conducted according to the procedure forcompound 1028, except using MeOH-EtOAc as the solvent, gave(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-((3-aminobenzo[d]isoxazol-6-yl)methyl)azetidine-2-carboxamidehydrochloride.

Step 3: To a solution of(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-((3-aminobenzo[d]isoxazol-6-yl)methyl)azetidine-2-carboxamide hydrochloride (160 mg,0.38 mmol) in anhyd MeCN (10 mL) under Ar was added DIEA (0.25 mL) andbromobenzylacetate (0.08 mL, 0.50 mmol). The mixture was stirred at roomtemp. for 15 h then concentrated under vacuum and re-dissolved in EtOAc.The solution was washed with H₂O and brine, dried (Na₂SO₄) andchromatographed with 55-100% EtOAc-hexanes to give 144 mg of benzyl((R)-2-((S)-2-(((3-aminobenzo[d]isoxazol-6-yl)methyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)glycinate.

Step 4: Benzyl((R)-2-((S)-2-(((3-aminobenzo[d]isoxazol-6-yl)methyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)glycinate was converted tocompound 1116 following the procedure of compound 1028, step 6.

Example 10: Preparation of(S)-1-((R)-2-Amino-2-cyclohexylacetyl)-N-((1-aminoisoquinolin-6-yl)methyl)azetidine-2-carboxamidedihydrochloride (1041)

Step 1: 6-(Aminomethyl)isoquinolin-1-amine and(S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxylic acid were coupledfollowing the procedure of compound 1116, step 1. After 15 h reactiontime, additional DIEA (1 equiv) was added and stirring was continued for24 h. Following concentration under vacuum, the residue was dissolved inEtOAc and washed with NaHCO₃ solution, H₂O, and brine then dried(Na₂SO₄). Chromatography (0-10% MeOH—CH₂Cl₂) gave tert-butyl((R)-2-((S)-2-(((1-aminoisoquinolin-6-yl)methyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)carbamate(51% yield).

Step 2: To a solution of tert-butyl((R)-2-((S)-2-(((1-aminoisoquinolin-6-yl)methyl)carbamoyl)azetidin-1-yl)-1-cyclohexyl-2-oxoethyl)carbamate(0.51 g, 1.0 mmol) in anhyd CH₂Cl₂ under Ar was added NMM (0.5 mL, 4.5mmol) and benzylchloroformate (0.2 mL, 1.4 mmol) dropwise. Afterstirring at room temp for 1.5 h, additional benzylchloroformate ((0.15mL, 1.0 mmol) was added and the mixture was stirred for 2.5 h. Aftercone under vacuum, EtOAc and saturated aqueous NaHCO₃ were added and thelayers were separated. The org layer was washed with brine and dried(Na₂SO₄). Chromatography (75-100% EtOAc-hexanes) provided benzyl(6-(((S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)isoquinolin-1-yl)carbamate(79% yield).

Step 3: The Boc group of benzyl(6-(((S)-1-((R)-2-((tert-butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)isoquinolin-1-yl)carbamatewas removed according to the procedure for compound 1116, step 2followed by aqueous extractive work-up (sat aqueous NaHCO₃/CH₂Cl₂) gavebenzyl(6-(((S)-1-((R)-2-amino-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)isoquinolin-1-yl)carbamate(88% yield).

Step 4: Benzyl(6-(((S)-1-((R)-2-amino-2-cyclohexylacetyl)azetidine-2-carboxamido)methyl)isoquinolin-1-yl)carbamate (163 mg, 0.31 mmol) was subjected tohydrogenolysis in MeOH with 10% Pd/C (24 mg) under 1 atm H₂. After thereaction did not proceed to completion with extended reaction time (42h); 6 M HCl (0.5 mL, 3 mmol) was added. The mixture was reacted under 1atm H₂ for 21 h then filtered (0.2 μM syringe filter). Chromatography ona 12 g Biotage C-18 column (5-30% MeCN—H₂O) gave 49 mg of compound 1041as a white solid in 40% yield.

Example 11: Preparation of(S)-1-((R)-2-Amino-2-cyclohexylacetyl)-N-(4-guanidinobutyl)azetidine-2-carboxamideDihydrochloride (1006)

Step 1: To an ice-cold solution of Boc-Agm (Z) (3.0 g, 8.2 mmol,synthesized according to the procedure of WO9429335) in EtOAc-MeOH (20mL, 1:1) was added 4 M HCl-dioxane (10 mL). After 10 min, the solutionwas allowed to warm to room temp and stirred for 3 h. The mixture wasconcentrated under vacuum and the residue was dissolved in EtOAc-MeOHand concentrated under vacuum. This procedure was repeated to givebenzyl N—[N-(4-aminobutyl)carbamimidoyl]carbamate hydrochloride as afoam (2.045 g, 82% yield).

Step 2:(S)-1-((R)-2-((tert-Butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxylicacid and benzyl N—[N-(4-aminobutyl)carbamimidoyl]carbamate hydrochloridewere coupled according to the procedure for compound 1116, step 1.Chromatography (0-6% MeOH—CH₂Cl₂) provided tert-butyl((R)-1-cyclohexyl-2-((S)-2-((4-(3-Cbz-guanidino)butyl)carbamoyl)azetidin-1-yl)-2-oxoethyl)carbamateas a white foam (435 mg, 84% yield).

Step 3: Boc removal according to the procedure for compound 1116, step 2provided intermediate(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-(4-(3-Cbz-guanidino)butyl)azetidine-2-carboxamidedihydrochloride as a white foam.

Step 4: Removal of the Cbz group of(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-(4-(3-Cbz-guanidino)butyl)azetidine-2-carboxamidedihydrochloride was conducted according to compound 1028, step 6followed by the addition of concd HCl (˜3 mmol), filtration (0.2 μMsyringe filter) and concentrated under vacuum gave an orange oil. A MeOHsolution of the crude product was treated with finely divided charcoaland heated at 30° C. for 30 min. After cooling to room temp, the mixturewas filtered (0.2 μM syringe filter) and concentrated under vacuum togive(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-(4-guanidinobutyl)azetidine-2-carboxamidedihydrochloride as a beige foam (306 mg).

Example 12: Preparation of(S)-1-((R)-2-Amino-2-cyclohexylacetyl)-N-(3-guanidinopropyl)azetidine-2-carboxamideHydrochloride (1004)

Step 1: 10-Oxa-2,4,8-triazadodecanoic acid,3-imino-11,11-dimethyl-9-oxo-, phenylmethyl ester (synthesized accordingto the procedure of WO9429335) was deprotected according to theprocedure for compound 1006, step 1 to give carbamic acid,[[(3-aminopropyl)amino]iminomethyl]-, benzyl ester hydrochloride as awhite foam.

Step 2:(S)-1-((R)-2-((tert-Butoxycarbonyl)amino)-2-cyclohexylacetyl)azetidine-2-carboxylicacid and carbamic acid, [[(4-aminopropyl)amino]iminomethyl]-, benzylester hydrochloride were coupled and subsequently deprotected accordingto the procedure for compound 1006 to give(S)-1-((R)-2-amino-2-cyclohexylacetyl)-N-(3-guanidinopropyl)azetidine-2-carboxamidehydrochloride as a white foam (279 mg, 74% yield for three steps).

Example 13: Preparation of(S)-2-((R)-2-Amino-2-(2,3-dihydro-1H-inden-2-yl)acetamido)-N-((1-aminoisoquinolin-6-yl)methyl)propanamideDihydrochloride (1088)

Step 1: Benzyl((R)-2-((tert-butoxycarbonyl)amino)-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-L-alaninate(3.6 g, 7.96 mmol, prepared according to the procedure for compound1116, step 1) was hydrogenated with 10% Pd/C in MeOH according to theprocedure for compound 1028, step 6. The crude material was crystallizedfrom warm EtOH-H₂O; the solid that was collected on a fritted funnel andrinsed with H₂O to give((R)-2-((tert-butoxycarbonyl)amino)-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-L-alanineas a white powder (2.45 g, 85% yield).

Step 2: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-L-alanine(291 mg, 0.80 mmol) in anhyd DMF (2.5 mL) was added6-(aminomethyl)isoquinolin-1-amine dihydrochloride (252 mg, 1.0 mmol)and DIEA (0.54 mL, 3.1 mmol) to give a tan suspension. HBTU (349 mg,0.92 mmol) was added in two aliquots then additional anhyd DMF (0.4 mL).After stirring for 50 min at room temp, additional HBTU (18 mg, 0.05mmol) was added. The reaction was stirred for 90 min then concentratedunder vacuum. The residue was dissolved in EtOAc-CH₂Cl₂ then washed with5% aqueous NaHCO₃ and brine, then dried (Na₂SO₄). Chromatography (0-10%MeOH—CH₂Cl₂) gave tert-butyl((R)-2-(((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-(2,3-dihydro-1H-inden-2-yl)-2-oxoethyl)carbamate(398 mg, 95% yield).

Step 3: To an ice-cold solution of tert-butyl((R)-2-(((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-(2,3-dihydro-1H-inden-2-yl)-2-oxoethyl)carbamate(130 mg, 0.25 mmol) in MeOH (2 mL) was added 4 M HCl-dioxane (3 mL). Themixture was stirred for 40 min then allowed to warm to room temperature.After stirring for 4 h total, the solution was concentrated undervacuum. The residue was dissolved in a minimal amount of MeOH andtriturated with Et₂O. The mixture was warmed for 30 min at 30-40° C.then cooled to room temp. The solid was collected on a fritted funneland rinsed with Et₂O. The solid was dried under vacuum at room temp togive(S)-2-((R)-2-amino-2-(2,3-dihydro-1H-inden-2-yl)acetamido)-N-((1-aminoisoquinolin-6-yl)methyl)propanamideas an off-white solid (107 mg, 93% yield).

Example 14: Preparation of(S)-2-((R)-2-Amino-2-(2,3-dihydro-1H-inden-2-yl)acetamido)-N-(4-(N-methylcarbamimidoyl)benzyl)propenamideDihydrochloride (1062)

Step 1:((R)-2-((tert-Butoxycarbonyl)amino)-2-(2,3-dihydro-1H-inden-2-yl)acetyl)-L-alaninewas coupled to 4-(aminomethyl)-N-methylbenzimidamide dihydrochloride(synthesized according to WO2003028729, except that one Boc protectinggroup was used in the synthetic sequence) were coupled according to theprocedure of compound 1088, step 2 at 15° C. to room temp for 16 h.After extractive workup with 10% MeOH—CH₂Cl₂, chromatography (0-10% (7 MNH₃-MeOH)—CH₂Cl₂) provided tert-butyl((R)-1-(2,3-dihydro-1H-inden-2-yl)-2-(((S)-1-((4-(N-methylcarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-2-oxoethyl)carbamatethat was contaminated with the dimethyl benzamidine derivative.Purification by HPLC (4-45%, then 70% MeCN—H₂O) gave moderate separationof the two products. Lyophilization of the purest fractions gavetert-butyl((R)-1-(2,3-dihydro-1H-inden-2-yl)-2-(((S)-1-((4-(N-methylcarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-2-oxoethyl)carbamateas a white solid (73 mg, 23% yield.

Step 2: tert-Butyl((R)-1-(2,3-dihydro-1H-inden-2-yl)-2-(((S)-1-((4-(N-methylcarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-2-oxoethyl)carbamatewas deprotected according to the procedure of compound 1088, step 3. Theresidue was triturated with Et₂O-EtOAc with sonication to give(S)-2-((R)-2-amino-2-(2,3-dihydro-1H-inden-2-yl)acetamido)-N-(4-(N-methylcarbamimidoyl)benzyl)propenamidedihydrochloride as a light yellow solid (62 mg).

Example 15: Preparation of(R)-2-Amino-N—((S)-1-((2-(6-aminopyridin-3-yl)ethyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1015)

Step 1: tert-ButylN-[(tert-butoxy)carbonyl]-N-(5-methylpyridin-2-yl)carbamate (synthesizedaccording to WO2010141406) was brominated following a modified procedurealso reported in WO2010141406 as follows. Tert-butylN-[(tert-butoxy)carbonyl]-N-(5-methylpyridin-2-yl)carbamate (2.118 g,6.87 mmol) was partially dissolved in CCl₄ (60 mL). To this mixture wasadded NBS (1.22 g, 6.86 mmol) and benzoyl peroxide (0.21 g, 0.65 mmol).The mixture was heated at 80° C. for 20 h. After cooling to room temp,the mixture was diluted with CH₂Cl₂ and washed with saturated aqueousNaHCO₃ 2×, 5% aqueous NaHCO₃ and brine then dried (Na₂SO₄) andconcentrated under vacuum to give crude di-tert-butyl5-(bromomethyl)pyridin-2-yliminodicarbonate (2.6 g).

Step 2: To a solution of crude di-tert-butyl5-(bromomethyl)pyridin-2-yliminodicarbonate (2.2 g) in CH₂Cl₂ (40 mL)was added H₂O, NaCN (0.85 g, 17.3 mmol) and Bu₄NI (6.4 g, 17.3 mmol).The mixture was stirred vigorously at room temp for 19 h then dilutedwith CH₂Cl₂ and washed with saturated aqueous NaHCO₃ 2×, H₂O and brine.Dried (Na₂SO₄) and concentrated under vacuum then chromatographed (0-40%EtOAc-hexanes) to give di-tert-butyl5-(cyanomethyl)pyridin-2-yliminodicarbonate (0.84 g).

Step 3: To a solution of di-tert-butyl5-(cyanomethyl)pyridin-2-yliminodicarbonate (370 mg, 1.1 mmol) in MeOH(5 mL) was added CoCl₂-6H₂O (292 mg, 1.2 mmol) and di-tert-butyldicarbonate (470 mg, 2.2 mmol). The solution was cooled over an ice/EtOHbath for 4 min, then NaBH₄ (165 mg, 4.4 mmol) was added in threealiquots over 25 min. The mixture was stirred for 20 min then allowed towarm to room temp and stirred for 75 min. The reaction was quenched with0.5 M KHSO₄ in 0.5 mL aliquots until pH=2. The aqueous mixture wasextracted with 5% MeOH—CH₂Cl₂ several times then the aqueous layer wasadjusted to pH 4-5 with the addition of several drops of 2 M NaOH.Additional extractions with CH₂Cl₂ were conducted. The combined organicswere washed with brine, dried (Na₂SO₄) and concentrated under vacuum togive a yellow oil. Chromatography (0-45% EtOAc-hexanes) gave tert-butyl(tert-butoxycarbonyl)(5-(2-((tert-butoxycarbonyl)amino)ethyl)pyridin-2-yl)carbamatethat was contaminated with 10% of the starting material (320 mg, 66%crude yield).

Step 4: tert-Butyl(tert-butoxycarbonyl)(5-(2-((tert-butoxycarbonyl)amino)ethyl)pyridin-2-yl)carbamate(320 mg, 0.73 mmol) was reacted with a concentrated solution of HCl-MeOH(4 mL) prepared by saturating MeOH with HCl (g). After stirring for 4 h,Et₂O was added and the mixture was concentrated under vacuum.Trituration with MeOH-Et₂O gave a ppt that was collected on a frittedfunnel and rinsed with Et₂O and hexanes. 5-(Aminoethyl)pyridin-2-aminedihydrochloride was isolated (135 mg, 76% yield).

Step 5: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninewas coupled with 5-(2-aminoethyl)pyridin-2-amine dihydrochloride toprovide tert-butyl((R)-1-(((S)-1-((2-(6-aminopyridin-3-yl)ethyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatefollowing the procedure for compound 1088, step 2 at 10° C. to room tempfor 3 h (94% yield).

Step 6: Deprotection of tert-butyl((R)-1-(((S)-1-((2-(6-aminopyridin-3-yl)ethyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewith HCl-MeOH afforded(R)-2-amino-N—((S)-1-((2-(6-aminopyridin-3-yl)ethyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride after crystallization from MeOH-MeCN (49 mg, 27% yield).

Example 16: Preparation of(R)-2-Amino-N—((S)-1-(((4-aminoquinazolin-7-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1060)

Step 1: 7-(Aminomethyl)quinazolin-4-amine was synthesized from7-bromoquinazolin-4-amine in two steps by the procedure reported inWO2015103317.

Step 2: tert-Butyl((R)-1-(((S)-1-(((4-aminoquinazolin-7-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas synthesized by coupling 7-(aminomethyl)quinazolin-4-amine and((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alanineaccording to the procedure for compound 1088, step 2 at 0-5° C.

Step 3: Deprotection of tert-butyl((R)-1-(((S)-1-(((4-aminoquinazolin-7-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewith MeOH and 3 M HCl-CPME provided(R)-2-amino-N—((S)-1-(((4-aminoquinazolin-7-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride as a white powder (50 mg, 96% yield).

Example 17: Preparation of(R)-2-Amino-N—((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)-N-methyl-4-(3-(trifluoromethyl)phenyl)butanamideDihydrochloride (1139)

Step 1:(R)-2-((tert-Butoxycarbonyl)amino)-4-(3-(trifluoromethyl)phenyl)butanoicacid was coupled to methyl methyl-L-alaninate according to the methodfor compound 1116, step 1 to afford methylN—((R)-2-((tert-butoxycarbonyl)amino)-4-(3-(trifluoromethyl)phenyl)butanoyl)-N-methyl-L-alaninate.

Step 2:N—((R)-2-((tert-Butoxycarbonyl)amino)-4-(3-(trifluoromethyl)phenyl)butanoyl)-N-methyl-L-alaninewas synthesized from methylN—((R)-2-((tert-butoxycarbonyl)amino)-4-(3-(trifluoromethyl)phenyl)butanoyl)-N-methyl-L-alaninateaccording to the procedure for ester hydrolysis for compound 1058.

Step 3:N—((R)-2-((tert-Butoxycarbonyl)amino)-4-(3-(trifluoromethyl)phenyl)butanoyl)-N-methyl-L-alaninewas coupled with 6-(aminomethyl)isoquinolin-1-amine dihydrochlorideaccording to the foregoing procedures to provide tert-butyl((R)-1-(((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)(methyl)amino)-1-oxo-4-(3-(trifluoromethyl)phenyl)butan-2-yl)carbamate.

Step 4: tert-Butyl((R)-1-(((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)(methyl)amino)-1-oxo-4-(3-(trifluoromethyl)phenyl)butan-2-yl)carbamatewas deprotected with MeOH and 3 M HCl-CPME according to the foregoingprocedures to give(R)-2-amino-N—((S)-1-(((1-aminoisoquinolin-6-yl)methyl)amino)-1-oxopropan-2-yl)-N-methyl-4-(3-(trifluoromethyl)phenyl)butanamidedihydrochloride.

Example 18: Preparation of2-Amino-N—((S)-1-(((2-amino-1H-benzo[d]imidazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate salt (1040)

Step 1: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninewas coupled with 6-(aminomethyl)-1H-benzo[d]imidazol-2-aminedihydrochloride according to the procedure of compound 1088, step 2except that the reaction was conducted at room temp and the6-(aminomethyl)-1H-benzo[d]imidazol-2-amine dihydrochloride was added tothe reaction mixture last. The reaction was stirred for 18 h after whichthe mixture was concentrated under vacuum. The residue was diluted withCH₂Cl₂ and washed with 5% aqueous NaHCO₃, dried (Na₂SO₄) andchromatographed with 10% MeOH (containing 7 M NH₃)—CH₂Cl₂ to givetert-butyl((R)-1-(((S)-1-(((2-amino-1H-benzo[d]imidazol-6-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatein 32% yield.

Step 2: tert-Butyl((R)-1-(((S)-1-(((2-amino-1H-benzo[d]imidazol-6-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas deprotected with HCl-MeOH as described in foregoing procedures togive2-amino-N—((S)-1-(((2-amino-1H-benzo[d]imidazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride. The compound was purified by HPLC (2-15-35-90%MeCN—H₂O) to give2-amino-N—((S)-1-(((2-amino-1H-benzo[d]imidazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedi-trifluoroacetate salt, isomer 2.

Example 19: Preparation of(R)-2-Amino-N—((S)-1-((2-(2-aminopyridin-4-yl)ethyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1016)

Step 1: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninewas coupled with 4-(2-aminoethyl)pyridin-2-amine dihydrochloride toprovide tert-butyl((R)-1-(((S)-1-((2-(2-aminopyridin-4-yl)ethyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamateaccording to the procedure of compound 1088, step 2, except that thereaction was conducted at 10-15° C. to room temp.

Step 2: tert-Butyl((R)-1-(((S)-1-((2-(2-aminopyridin-4-yl)ethyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas deprotected with HCl-MeOH according to the foregoing procedures togive compound 1016 (80 mg, 89% yield).

Example 20: Preparation of(R)-2-Amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(4-(trifluoromethyl)phenyl)butanamideDihydrochloride (1119)

Step 1: To a solution of(R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoicacid (500 mg, 1.44 mmol) in anhydrous MeCN (30 mL) was added HOBt (1.1equiv, 1.58 mmol), DIEA (4.0 equiv, 5.76 mmol) and EDC (1.1 equiv, 1.58mmol) with stirring at room temp. for 30 min. Benzyl L-alaninatehydrochloride (1.1 equiv, 1.58 mmol) was added and stirred overnight.The solution was evaporated to dryness and the residue was partitionedwith EtOAc (60 mL) and 10% KHSO₄ (50 mL). The organic layer wasseparated and washed with H₂O (30 mL), saturated Na₂CO₃ (60 mL), dried(Na₂SO₄) and evaporated leaving benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoyl)-L-alaninate(512 mg, 70%) as an oil pure enough to use in the next step.

Step 2: A solution of benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoyl)-L-alaninate(512 mg, 1.01 mmol) in MeOH (20 mL) was degassed with a stream of Ar for2-3 min. 10% Pd/C (50 mg) was added and a vacuum was pulled for approx.3 min. A balloon of H₂ was added and the reaction was monitored for theconsumption of starting material (typically 1-4 h). The catalyst wasremoved by filtration and the solution was evaporated to dryness leaving((R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoyl)-L-alanineas a fluffy white solid (420 mg, 100%).

Step 3: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoyl)-L-alanine(400 mg, 0.956 mmol) in CH₂Cl₂ (15 mL) was added NHS (1.1 equiv, 1.05mmol) with stirring at room temp. until dissolved. DCC (1.1 equiv, 1.05mmol) was added and stirred for 1.0 h. This mixture was poured into aseparatory funnel containing saturated NaHCO₃ (15 mL), and benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate hydrochloride (1.2equiv, 1.15 mmol) and then shaken for 5 min. The organic layer wasfiltered over a bed of anhyd Na₂SO₄ and evaporated to dryness. Flashchromatography (3% 7 N NH₃ in MeOH/CH₂Cl₂) gave tert-butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-(4-(trifluoromethyl)phenyl)butan-2-yl)carbamateas an oil (477 mg, 73%). [In certain cases, products were able to becollected by filtration after a reduction in volume of the CH₂Cl₂ layer.These products contained a small amount of DCU which was removed in thefinal step of the synthesis by filtration from H₂O.]

Step 4: To tert-butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-(4-(trifluoromethyl)phenyl)butan-2-yl)carbamate(460 mg, 0.673 mmol) was added a solution of MeOH/HCl (5.0 mL, 227 mgHCl/mL) with stirring at room temp while monitoring for the consumptionof starting material. The solution was evaporated to dryness and MeOH(15 mL) was added and evaporated to dryness giving benzyl((4-(((S)-2-((R)-2-amino-4-(4-(trifluoromethyl)phenyl)butanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride as a white solid pure enough to use in the next step (420mg, 100%).

Step 5: A solution of benzyl((4-(((S)-2-((R)-2-amino-4-(4-(trifluoromethyl)phenyl)butanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride (420 mg, 0.677 mmol) in MeOH (10 mL) was degassed with astream of Ar for 2-3 min. 10% Pd/C (50 mg) was added and a vacuum waspulled for approx. 3 min. A balloon of H₂ was applied and the reactionwas monitored for the consumption of starting material (typically 1-2h). The catalyst was removed by filtration then 4 drops of concentratedHCl was added and the solution was evaporated to dryness. To the residuewas added H₂O (2-3 mL). The mixture was filtered then and lyophilized,giving(R)-2-amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(4-(trifluoromethyl)phenyl)butanamidedihydrochloride as an off white solid (350 mg, 100%).

Example 21: Preparation of(R)-2-Amino-N—((S)-1-((4-(N-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1157)

Step 1: To a solution of tert-butyl((R)-1-(((S)-1-((4-cyanobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(660 mg, 1.42 mmol, prepared according to compound 1119, step 3 using4-cyanobenzyl amine HCl in MeOH (20 mL) was added hydroxylamine HCl (1.5equiv, 2.13 mmol) and Et₃N (1.5 equiv, 2.13 mmol). This mixture washeated at reflux for 4 h, evaporated to dryness, and then partitionedbetween H₂O (15 mL) and EtOAc (2×30 mL.) The combined organic layerswere dried over anhyd Na₂SO₄ and evaporated. Chromatography (50%EtOAc-hexanes) gave tert-butyl((R)-1-(((S)-1-((4-(N-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamateas a white solid (417 mg, 59%).

Step 2: The intermediate was deprotected according to the procedure forcompound 1119, step 4, to provide(R)-2-amino-N—((S)-1-((4-(N-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride (i.e., compound 1157).

Example 22: Preparation of(R)—N—(S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamideDi-trifluoroacetate (1032)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-hydroxy-4-phenylpyrrolidine-2-carboxamidedihydrochloride (45 mg, 0.093 mmol) was stirred in TFA (5.0 mL) for 48 hat room temp. The solution was evaporated to dryness and the residue wassubjected to purification using reverse phase HPLC (5-45-75-90%MeCN—H₂O).(R)—N—(S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamidedi-trifluoroacetate was isolated as a white solid (15 mg, 26% yield).

Example 23: Preparation of(2R)-2-Amino-N-(1-((4-carbamimidoylbenzyl)amino)-3-fluoro-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1050)

Step 1: tert-Butyl(1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-fluoro-1-oxopropan-2-yl)carbamatewas synthesized from 2-((tert-butoxycarbonyl)amino)-3-fluoropropanoicacid and benzyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatehydrochloride according to the procedure for compound 1119, step 3.

Step 2: tert-Butyl(1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-fluoro-1-oxopropan-2-yl)carbamatewas deprotected according to the procedure for compound 1119, step 4 togive benzyl ((4-((2-amino-3-fluoropropanamido)methyl)phenyl)(imino)methyl)carbamate hydrochloride.

Step 3: Benzyl((4-((2-((R)-2-amino-4-phenylbutanamido)-3-fluoropropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride was synthesized from benzyl((4-((2-amino-3-fluoropropanamido)methyl)phenyl) (imino)methyl)carbamatehydrochloride and (R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoicacid according to the procedure for compound 1119, step 3.

Step 4: Benzyl((4-((2-((R)-2-amino-4-phenylbutanamido)-3-fluoropropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride was synthesized from benzyl((4-((2-((R)-2-amino-4-phenylbutanamido)-3-fluoropropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride according to the procedure for compound 1119, step 4.

Step 5:(2R)-2-Amino-N-(1-((4-carbamimidoylbenzyl)amino)-3-fluoro-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride (1050) was synthesized from benzyl((4-((2-((R)-2-amino-4-phenylbutanamido)-3-fluoropropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride according to the procedure for compound 1119, step 5.

Example 24: Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(cyclohexylamino)-4-phenylbutanamideDihydrochloride (1130)

Step 1: Benzyl ((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate (1.9 g, 41% yield in 4 steps) wassynthesized by a method similar to that used for compound 1119, exceptthe crude product was purified by chromatography (10% MeOH—CH₂Cl₂ andthen 5% 7 N NH₃ in MeOH—CH₂Cl₂).

Step 2: To a 20-mL scintillation vial, benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate(55.1 mg, 0.107 mmol) was added and followed by THF (400 μL). Thesolution was treated with cyclohexanone (15 μL, 0.145 mmol) at room tempfollowed by Na(OAc)₃ solid (32 mg, 0.151 mmol) and HOAc (10 μL, 0.175mmol). After purging with N₂, the vial was capped. The reaction wasstirred at room temp for 4 h and quenched with about 15 mL saturatedNaHCO₃ solution. The resulting mixture was extracted with 15 mL CH₂Cl₂(3 times). The organic layers were combined, washed with brine, dried(Na₂SO₄) vacuum filtered, and evaporated under vacuum. The crude productwas dissolved in CH₂Cl₂ and adsorbed on silica gel. Purification bychromatography (0-5% MeOH—CH₂Cl₂) gave benzyl((4-(((S)-2-((R)-2-(cyclohexylamino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate(44 mg, 69% yield).

Step 3: To a solution of benzyl((4-(((S)-2-((R)-2-(cyclohexylamino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate(44 mg, 0.0736 mmol) in MeOH (1.0 mL) was treated with 10% Pd/C (8.1 mg,0.00761 mmol) at room temp. Air was removed from the reaction apparatusby in-house N₂ line (5 times). H₂ was added via a balloon while stirringovernight. The reaction was filtered through a 0.25 m syringe filter.Volatiles were evaporated under vacuum to give(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(cyclohexylamino)-4-phenylbutanamide,compound 1130 (25.3 mg, 69% yield).

Example 25: Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-hydroxybenzyl)amino)-4-phenylbutanamideDihydrochloride (1140)

(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-hydroxybenzyl)amino)-4-phenylbutanamide(17.7 mg, 30% yield in 2 steps) was synthesized by a method similar tothat used for compound 1130, except the crude product was purified byreverse phase HPLC (5-45-75-90% MeCN—H₂O).

Example 26: Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2-((4-(piperazin-1-yl)benzyl)amino)butanamide,Trifluoroacetate Salt (1148)

Step 1: A clear solution of 4-(piperazin-1-yl)benzaldehyde (502 mg, 2.68mmol) in CH₂Cl₂ (10 mL) was treated with DIEA (0.900 mL, 5.17 mmol) atroom temp under N₂ and the reaction changed to clear yellow solution.Benzyl chloroformate (0.450 mL, 3.19 mmol) was added. The reactiongradually changed to deep clear red solution. After stirring at roomtemp overnight, the reaction was washed with 20 mL 1 N HCl solution (2times). The organic layer was washed with brine, dried (Na₂SO₄), vacuumfiltered, and evaporated under vacuum. Purification by flashchromatography (0-100% EtOAc-hexanes) gave benzyl4-(4-formylphenyl)piperazine-1-carboxylate (606 mg, 70% yield).

Step 2:(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2-((4-(piperazin-1-yl)benzyl)amino)butanamide(3.4 mg, 2.8% yield in 2 steps) was synthesized by a method similar tocompound 1130, steps 1 and 2, except the crude product was purified byreverse phase HPLC condition (5-15-90% MeCN—H₂O) similar to that usedfor compound 1140.

Example 27: Preparation of(R)-2-((5-Aminopentyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideTrihydrochloride (1132)

Step 1: tert-Butyl(5-(((R)-1-(((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)pentyl)carbamatewas synthesized by a method similar to step 1 that used for compound1130 (461.4 mg, 63% yield).

Step 2: Benzyl((4-(((S)-2-((R)-2-((5-aminopentyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate(crude) was synthesized by a method similar to that used for compound1119.

Step 3:(R)-2-((5-Aminopentyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidewas synthesized by a method similar to step 2 used for compound 1130(18.4 mg, 21% yield in 2 steps) except the crude product was purified byreverse phase HPLC (5-45-75-90% MeCN—H₂O); (18.4 mg, 21% yield in 2steps).

Example 28: Preparation of(R)-2-(((R)-2-Amino-3-phenylpropyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide,Tri-trifluoroacetate Salt (1144)

(R)-2-(((R)-2-Amino-3-phenylpropyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidewas synthesized by a method similar to that used for compound 1132except the crude product was purified by reverse phase HPLC condition(5-60-90% MeCN—H₂O); (13.6 mg, 12% yield in 3 steps).

Example 29: Preparation of(S)-2-(((R)-2-Amino-4-phenylbutyl)amino)-N-(4-carbamimidoylbenzyl)propanamideDihydrochloride (1013)

Step 1: A solution of(R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoic acid (694.9 mg, 2.49mmol) in THF (1 mL) was treated with 1 M borane-tetrahydrofuran complexsolution (4.2 mL, 4.2 mmol) at 0° C. in an ice bath under N₂. Gas wasproduced moderately. The reaction was warmed to room temp while stirringfor 4 h. H₂O was added slowly via syringe. Gas was produced violently.The resulting mixture was extracted with 30 mL CH₂Cl₂ (3 times) afteradding 30 mL saturated NH₄Cl solution. The organic layers were combined,dried (Na₂SO₄), vacuum filtered, and evaporated under vacuum.Purification by chromatography (0-100% EtOAc-hexanes) gave tert-butyl(R)-(1-hydroxy-4-phenylbutan-2-yl)carbamate (263.4 mg, 40% yield).

Step 2: A solution of tert-butyl(R)-(1-hydroxy-4-phenylbutan-2-yl)carbamate (263.4 mg, 0.993 mmol) inCH₂Cl₂ (17 mL) was treated with Dess-Martin periodinane (468.9 mg, 1.10mmol, 1.1 eq) at 0° C. The reaction was stirred at the same temperaturefor 2.5 h. The reaction became opaque and was added to a solution of 1 MNa₂S20₃ (20 mL) and 1 M NaHCO₃ (20 mL) at room temp. The resultingmixture was stirred at room temp for 15 min and became colorless. Theorganic was separated and the aqueous layer was extracted with CH₂Cl₂(2×20 mL). The organic layer was combined, washed once with saturatedNaHCO₃ solution, dried over Na₂SO₄, vacuum filtered, and evaporatedunder vacuum. Purification by chromatography (0-100% EtOAc-hexanes) gavetert-butyl (R)-(1-oxo-4-phenylbutan-2-yl)carbamate (199 mg, 76%).

Step 3: A solution of tert-butyl (R)-(1-oxo-4-phenylbutan-2-yl)carbamate(199 mg, 0.756 mmol) in THF (1.8 mL) was treated with benzyl L-alaninatehydrochloride (102.6 mg, 0.476 mmol) followed by DIEA (240 μL, 1.38mmol). The resulting colorless solution was treated with NaBH(OAc)₃(148.6 mg, 0.701 mmol) and HOAc (85 μL, 1.49 mmol). After purging withN₂, the vial was capped. The reaction was stirred at room temp for 4 hand quenched with about 20 mL saturated NaHCO₃ solution. The resultingmixture was extracted with 20 mL CH₂Cl₂ (3 times). The organic layerswere combined, washed with brine, dried (Na₂SO₄), vacuum filtered, andevaporated under vacuum. The crude product was dissolved in CH₂Cl₂ andadsorbed onto silica gel. Purification by chromatography (0-100%EtOAc-hexanes) gave benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutyl)-L-alaninate (127 mg,63% yield).

Step 4: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutyl)-L-alanine (99mg, 100% yield) was synthesized by a method similar to step 2, used forcompound 1130.

Step 5: tert-Butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-4-phenylbutan-2-yl)carbamate(66.8 mg, 38% yield) was synthesized by a method similar to that usedfor compound 1119, except the crude product was purified bychromatography (10% MeOH—CH₂Cl₂).

Step 6: Benzyl((4-(((S)-2-(((R)-2-amino-4-phenylbutyl)amino)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized by a method similar to that used for compound 1119,except the crude product was purified by flash chromatography (10%MeOH—CH₂Cl₂ and then 5% 7 N NH₃ in MeOH—CH₂Cl₂). This procedure yielded15.1 mg (27% yield) of material.

Step 7:(S)-2-(((R)-2-Amino-4-phenylbutyl)amino)-N-(4-carbamimidoylbenzyl)propanamide(i.e., compound 1013) was synthesized by a method similar to step 2 thatused for compound 1130, except the crude product was purified by reversephase HPLC (2-15-35-90% MeCN—H₂O) similar to that used for compound1140. This procedure yielded 10.3 mg (72% yield) of material.

Example 30: Preparation of(R)-2-Amino-N—((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideHydrochloride (1031)

(R)-2-Amino-N—((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidewas prepared following similar protocols as reported for compound 1119,steps 1-4 using the appropriate starting materials.

Example 31: Preparation of(S)-1-((R)-2-Amino-4-phenylbutanoyl)-N-(5-chloro-2-hydroxybenzyl)pyrrolidine-2-carboxamideHydrochloride (1079)

Steps 1-2:((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-proline wasprepared following similar protocols as compound 1028, but with steps1-2 using the appropriate starting materials.

Steps 3-4:(S)-1-((R)-2-Amino-4-phenylbutanoyl)-N-(5-chloro-2-hydroxybenzyl)pyrrolidine-2-carboxamidewas prepared following similar protocols as reported for compound 1060,step 2 using the appropriate starting materials.

Example 32: Preparation of(R)-2-Amino-N—((S)-1-((5-chloro-2-(2-(ethylamino)-2-oxoethoxy)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide,Trifluoroacetate Salt (1137)

Step 1: tert-Butyl((R)-1-(((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(436 mg, 0.89 mmol, as prepared for compound 1031) was suspended in DMF(4 mL) and treated with ethyl bromoacetate (148 μL, 1.34 mmol) andCs₂CO₃ (725 mg, 2.23 mmol). The reaction mixture was allowed to stir for18 h, then diluted with EtOAc and washed with H₂O, 5% aqueous LiCl andbrine. The organic layer was dried over MgSO₄ and concentrated undervacuum, then purified by chromatography (40-80% EtOAc-hexanes) to yieldethyl2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)acetateas a white powder (370 mg, 72% yield).

Step 2: A reaction vessel was charged with ethyl2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)acetate(370 mg, 0.64 mmol), LiOH (31 mg, 1.28 mmol), THF (3 mL) and H₂O (3 mL).The reaction mixture was allowed to stir at room temp for 4 h, then THFwas removed under vacuum and the residue was treated with 10% aq. KHSO₄(3 mL). The resulting ppt was filtered and washed with water and hexanesto provide2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)aceticacid as a white solid (281 mg, 80% yield).

Steps 3-4:2-(4-Chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)aceticacid (24 mg, 0.04 mmol) and HOBt (5.9 mg, 0.044 mmol) were dissolved inDMF (1 mL). EDC (8.4 mg, 0.044 mmol) was then added in a single portion,followed by ethylamine (2 M in THF, 150 μL) and DIEA (21 μL, 0.12 mmol).The resulting solution was allowed to stir at room temp for 60 h. Thereaction mixture was then diluted with EtOAc, washed with 10% aqueousKHSO₄, 5% aqueous LiCl, saturated NaHCO₃ (×2) and brine. The crudemixture was treated with HCl in MeOH and filtered through diatomaceousearth, then purified by preparative HPLC (5% to 95% MeCN in H₂Ocontaining 0.1% TFA) to provide(R)-2-amino-N—((S)-1-((5-chloro-2-(2-(ethylamino)-2-oxoethoxy)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideas a white solid (2.4 mg, 11% yield).

Example 33. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1230)

Step 1: To a solution of(2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpiperidine-2-carboxylic acid(5.0 g, 16.4 mmol) in MeCN (300 mL, 0.05 M) was added HOBt (2.g, 3.77mmol), DIEA (11.4 mL, 13.7 mmol), and EDC (2.8 g, 3.77 mmol). Afterstirring for 30 min at room temperature, benzyl L-alanine hydrochloride(814 mg, 18 mmol) was added and stirred for 16 h. The reaction mixturewas conc in vacuo and the residue was partitioned with EtOAc and 10%KHSO₄ solution. The organic layer was separated and washed with H₂O andsaturated aq NaHCO₃. The organic layer was dried over anhyd Na₂SO₄ andconc under vacuum. The residue was purified by chromatography (0-20%EtOAc-hexanes; the 3^(rd) UVActive material eluting from the column) togive tert-butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(2.59 g, 34% yield).

Step 2: A solution of tert-butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(2.59 mg, 5.54 mmol) was degassed with a stream of Ar for 2 min. 10%Pd/C (130 mg) was added and a vacuum was pulled for 1 min. A balloon ofH₂ was added and the reaction was monitored for the consumption ofstarting material for 1.5 h. The catalyst was removed by filtration andthe solution was evaporated to give((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpiperidine-2-carbonyl)-L-alanine(1.8 g, 86%).

Step 3: tert-Butyl(2R,4S)-2-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylatewas synthesized according to the procedure for compound 0194.

Step 4: Benzyl(imino(4-(((S)-2-((2R,4S)-4-phenylpiperidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamatehydrochloride was synthesized according to the procedure for compound0195.

Step 5:(2R,4S)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidedihydrochloride was synthesized according to the procedure for compound0196.

Example 34. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamideDihydrochloride (1231)

Step 1: To a solution of dioxane: 2 M K₂CO₃ (1:1, 116 ml total) wasadded methyl 4-bromopicolinate 10.0 g (46.29 mmol) and m-tolylboronicacid (55.6 mmol, 1.2 eq.). The solution was degassed with a stream of Arfor 5 min. Pd(PPh₃)₄ (0.05 eq.) was added and the solution was refluxedfor 48 h. Dioxane was removed by evaporation followed by the addition ofH₂O (50 ml) and EtOAc (100 ml) with stirring. The aqueous layer wasseparated, and the pH adjusted to approx. 5 with the addition of solidKHSO₄. The product was collected by filtration, washed with H₂O anddried giving 4-(m-tolyl)picolinic acid (9.07 g, 92% yield).

Step 2: To a solution of 4-(m-tolyl)picolinic acid (9.05 g., 42.4 mmol)in anhyd MeOH (50 ml) was added H₂SO₄ (5 ml) with refluxing for 24 h.MeOH was removed by evaporation and the residue partitioned between sat.NaHCO₃ and CH₂Cl₂. The organic layer was dried over Na₂SO₄ andevaporated. Column chrom. (40% EtOAc/hexanes) gave methyl4-(m-tolyl)picolinate (6.05 g, 63% yield) as a yellow oil.

Step 3: To a solution of acetic acid (40 ml) was added methyl4-(m-tolyl)picolinate (2.4 g, 10.6 mmol) with degassing with Ar for 2min. PtO₂ (240 mg) was added and a vacuum pulled for 5 min. A balloon ofH₂ was added with stirring for 26 h. The catalyst was removed byfiltration followed by evaporation. Purification by chromatography (1%MeOH—CH₂Cl₂) gave methyl 4-(m-tolyl)piperidine-2-carboxylate (1.6 g, 65%yield) as an oil.

Step 4: To a solution of THF-sat. NaHCO₃ (1:1, 35 ml total) was addedmethyl 4-(m-tolyl)piperidine-2-carboxylate (1.6 g, 6.9 mmol) anddi-tert-butyl dicarbonate (1.05 equiv, 7.25 mmol) with stirringovernight. THF was removed by evaporation with extraction with CH₂Cl₂(2×30 ml). The organic layer was dried over Na₂SO₄ and evaporated todryness. 1-(tert-Butyl) 2-methyl 4-(m-tolyl)piperidine-1,2-dicarboxylate(2.34 g, 100% yield) was used in the next step.

Step 5: To a solution of THF-H₂O (1:1, 30 ml) was added 1-(tert-butyl)2-methyl 4-(m-tolyl)piperidine-1,2-dicarboxylate (2.34 g, 7.0 mmol) andLiOH (35.0 mmol, 5.0 equiv.) with stirring for 6 h. THF was removed byevaporation and the pH adjusted to 5 with 10% KHSO₄. The product wascollected by filtration, washed with H₂O and dried.1-(tert-Butoxycarbonyl)-4-(m-tolyl)piperidine-2-carboxylic acid (1.81 g,81% yield) as a pale yellow solid.

Steps 6-11:(2R,4S)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound (1230). Thethird UVActive material eluting from the column in step 6 was carriedforward.

Example 35. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((2-(4-methylpiperazin-1-yl)benzyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1232)

Step 1: Benzyl(imino(4-(((S)-2-((R)-2-((2-(4-methylpiperazin-1-yl)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl(imino(4-(((S)-2-((R)-2-((2-(4-methylpiperazin-1-yl)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)methyl)carbamateaccording to the procedure for compound 1130, step 3 afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((2-(4-methylpiperazin-1-yl)benzyl)amino)-4-phenylbutanamide.

Step 3:(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((2-(4-methylpiperazin-1-yl)benzyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt was formed according to the procedure forcompound (1368), step 2.

Example 36. Preparation of(R)-2-((4-(1H-Tetrazol-5-yl)benzyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate salt (1233)

Step 1: Benzyl((4-(((S)-2-((R)-2-((4-(1H-tetrazol-5-yl)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-(1H-tetrazol-5-yl)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded(R)-2-((4-(1H-tetrazol-5-yl)benzyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 37. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)-1H-pyrrole-2-carboxamide(1234)

Step 1: In a 50 mL round bottom flask equipped with a stir bar andseptum was added methyl 4-iodo-1H-pyrrole-2-carboxylate (300 mg, 1.19mmol), 1-naphthyl boronic acid (246 mg, 1.43), Pd(OAc)₂ (13 mg, 0.06mmol), potassium carbonate (330 mg, 2.39 mmol), acetone (2.7 mL) andwater (1.3 mL). The resulting mixture was degassed by bubbling N₂through the solution for 5 min. The reaction was then heated to 75° C.for 5 h. Upon cooling to room temperature, the reaction solution wasfiltered through diatomaceous earth, eluted with EtOAc, concentrated andpurified by chromatography using EtOAc-hexanes to afford methyl4-(naphthalen-1-yl)-1H-pyrrole-2-carboxylate (260 mg, 86% yield) as acolorless solid.

Step 2: 4-(Naphthalen-1-yl)-1H-pyrrole-2-carboxylic acid (180 mg, 82%)was synthesized from methyl 4-(naphthalen-1-yl)-1H-pyrrole-2-carboxylate(260 mg, 1.03 mmol) according to the procedure for compound (1328), step1.

Step 3: To a solution of (tert-butoxycarbonyl)-L-alanine (300 mg, 1.58mmol) in CH₂Cl₂ (11 mL) was added NHS (200 mg, 1.74 mmol) with stirringat ambient temperature until dissolution. DCC (359 mg, 1.74 mmol) wasadded and stirred for 1.0 h. This mixture was poured into a separatoryfunnel containing sat. NaHCO₃ (10 mL), and benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate hydrochloride (540 mg,1.90 mmol) and then shaken for 5 min. The organic layer was filteredover a bed of anhyd Na₂SO₄ and evaporated to dryness. Flashchromatography using EtOAc-hexanes gave tert-butyl(S)-(1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamateas a solid (560 mg, 80% yield).

Step 4: Benzyl(S)-((4-((2-aminopropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride (380 mg, 90%) was synthesized from tert-butyl(S)-(1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamate(560 mg, 1.23 mmol) according to the procedure for compound (1304), step6.

Step 5: Benzyl(S)-(imino(4-((2-(4-(naphthalen-1-yl)-1H-pyrrole-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(35 mg, 45% yield) was synthesized from benzyl(S)-((4-((2-aminopropanamido)methyl)phenyl)(imino)methyl)carbamatehydrochloride (60 mg, 0.17 mmol) according to the procedure for compound(1304), step 7.

Step 6:(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)-1H-pyrrole-2-carboxamide(25.3 mg, 94% yield) was synthesized from benzyl(S)-(imino(4-((2-(4-(naphthalen-1-yl)-1H-pyrrole-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(35 mg, 0.06 mmol) according to the procedure for compound (1304), step4.

Example 38. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-fluoro-4-methylphenyl)-1H-pyrrole-2-carboxamide(1235)

(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-fluoro-4-methylphenyl)-1H-pyrrole-2-carboxamidewas synthesized according to the procedures for compound (1234).

Example 39. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-(2-hydroxyethoxy)benzyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1236)

Step 1: Benzyl((4-(((S)-2-((R)-2-((4-(2-hydroxyethoxy)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-(2-hydroxyethoxy)benzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-(2-hydroxyethoxy)benzyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 40. Preparation of(R)-2-amino-N—((S)-1-((5-chloro-2-(2-((3-hydroxypropyl)amino)-2-oxoethoxy)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideHydrochloride (1237)

Step 1: tert-Butyl((R)-1-(((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(436 mg, 0.89 mmol, as prepared for compound 1031) was suspended in DMF(4 mL) and treated with ethyl bromoacetate (148 μL, 1.34 mmol) andCs₂CO₃ (725 mg, 2.23 mmol). The reaction mixture was allowed to stir for18 h, then diluted with EtOAc and washed with H₂O, 5% aqueous LiCl andbrine. The organic layer was dried over MgSO₄ and concentrated undervacuum, then purified by chromatography (40-80% EtOAc-hexanes) to yieldethyl2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)acetateas a white powder (370 mg, 72% yield).

Step 2: A reaction vessel was charged with ethyl2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)acetate(370 mg, 0.64 mmol), LiOH (31 mg, 1.28 mmol), THF (3 mL) and H₂O (3 mL).The reaction mixture was allowed to stir at room temp for 4 h, then THFwas removed under vacuum and the residue was treated with 10% aq. KHSO₄(3 mL). The resulting ppt was filtered and washed with water and hexanesto provide2-(4-chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)aceticacid as a white solid (281 mg, 80% yield).

Step 3:2-(4-Chloro-2-((4S,7R)-4,11,11-trimethyl-3,6,9-trioxo-7-phenethyl-10-oxa-2,5,8-triazadodecyl)phenoxy)aceticacid (51 mg, 0.09 mmol) and NHS (14 mg) were dissolved in ACN (1 mL).DCC (14 mg, 0.1 mmol) was then added in a single portion, followed by3-aminopropan-1-ol (22 μL, 0.29 mmol) and DIEA (47 p L, 0.27 mmol). Theresulting solution was allowed to stir at room temp for 16 h. Thereaction mixture was then diluted with EtOAc, washed with 10% aq KHSO₄,brine and sat. aq NaHCO₃. The organic layer was dried over Na₂SO₄ andconcentrated under vacuum, then purified by chromatography (7-9%MeOH—CH₂Cl₂) to yield tert-butyl((R)-1-(((S)-1-((5-chloro-2-(2-((3-hydroxypropyl)amino)-2-oxoethoxy)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamateas a colorless oil (25 mg, 44% yield).

Step 4:((R)-1-(((S)-1-((5-Chloro-2-(2-((3-hydroxypropyl)amino)-2-oxoethoxy)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatecarbamate was deprotected according to the procedure for compound 1119,step 4 to provide the title compound as a white solid (21 mg, 95%yield).

Example 41. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(4-methoxyphenyl)-1H-pyrrole-2-carboxamideTrifluoroacetate salt (1238)

(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(4-methoxyphenyl)-1H-pyrrole-2-carboxamidetrifluoroacetate salt was synthesized according to the procedures forcompound (1234), except that the final product was purified usingreverse-phase HPLC.

Example 42. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-5-methyl-4-phenyl-1H-pyrrole-2-carboxamideTrifluoroacetate salt (1239)

Step 1: NIS (3.77 g, 16.7 mmol) was added to a stirring solution ofmethyl 2-acetamidoacrylate (2 g, 13.9 mmol) in 2% TFA in CH₂Cl₂ (74 mLwith 1.5 mL TFA). The mixture was stirred at ambient temperatureovernight. The mixture was cooled over an ice bath before triethylamine(6 mL) was added slowly. The mixture was allowed to stir for a further 1h. The mixture was concentrated and taken up in CH₂Cl₂, washed with 1 MKHSO₄, water and brine before concentrating and purifying bychromatography on silica (hexanes/ethyl acetate 1:1) to obtain methyl(Z)-2-acetamido-3-iodoacrylate as a yellow-brown solid (1.50 g, 40%yield).

Step 2: Methyl (Z)-2-acetamido-3-iodoacrylate (500 mg, 1.86 mmol), LiCl(78.4 mg, 1.86 mmol), K₂CO₃ (1.28 g, 9.29 mmol) and Pd(OAc)₂ (42 mg,0.18 mmol) were dissolved in DMF (18 mL) and treated with theprop-1-yn-1-ylbenzene (648 mg, 5.57 mmol). The solution was degassed,placed under Argon atmosphere, and heated to 65° C. with stirring for 12h. The solution was filtered to remove solids, diluted with EtOAc (50mL), washed with water (25 mL), brine (25 mL), and the organic layerdried over Na₂SO₄. After conc in vacuo, chromatography (EtOAc-hexanes)afforded methyl 5-methyl-4-phenyl-1H-pyrrole-2-carboxylate (85 mg, 30%yield) and by-product (75 mg, 25% yield).

Step 3: 5-Methyl-4-phenyl-1H-pyrrole-2-carboxylic acid (40 mg, 85%yield) was synthesized from methyl5-methyl-4-phenyl-1H-pyrrole-2-carboxylate (45 mg, 0.21 mmol) accordingto the procedure for compound (1328), step 1.

Step 4:(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-5-methyl-4-phenyl-1H-pyrrole-2-carboxamidetrifluoroacetate salt was synthesized according to the procedures forcompound (1234), step 5 to step 6, except that the final product waspurified using reverse-phase HPLC.

Example 43. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4,5-diphenyl-1H-pyrrole-2-carboxamide(1240)

(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4,5-diphenyl-1H-pyrrole-2-carboxamidewas synthesized according to the procedures for compound (1239).

Example 44. Preparation of(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamideDihydrochloride (1241)

(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound (1231) (9). Thefirst UVActive material eluting from the column in step 6 was carriedforward.

Example 45. Preparation of(2R,4R)—N—((S)-1-((5-Chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(1242)

Steps 1-2: To a solution of((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(22 mg, 0.06 mmol) and 2-(aminomethyl)-4-chlorophenol hydrobromide (15mg, 0.06 mmol) in anhyd DMF (1 mL) at 0° C. was added HBTU (349 mg, 0.92mmol) and DIEA (31 μL, mmol). The reaction mixture was slowly warmed toambient temperature and stirred for 2 h, then diluted with EtOAc andwashed with 10% aq KHSO₄ and brine. The organic layer was dried overNa₂SO₄ and concentrated under vacuum, then purified by chromatography(70% EtOAc-hexanes) to provide tert-butyl(2R,4R)-2-(((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylateas a colorless oil. The residue was then taken up in MeOH (1 mL) andtreated with 3 M HCl in CPME (2 mL). After 4h, the reaction mixture wasconcentrated and purified by chromatography (7% MeOH/CH₂CL₂ containing2.5% 7 N NH₃-MeOH) to yield the title compound as a white solid (12.2mg, 51% yield over 2 steps).

Example 46. Preparation of(R)-2-Amino-N—((S)-1-(((6-amino-4-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1243)

Step 1: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alanine (152 mg,0.43 mmol) in anhyd DMF (3.5 mL) under Ar was added DIEA (0.10 mL, 0.57mmol) and 5-(aminomethyl)-4-methylpyridin-2-amine (65 mg, 0.47 mmol).The mixture was cooled over ice then HBTU (172 mg, 0.45 mmol) was added:the reaction was stirred for 30 min then stored at 2-8° C. overnight.The reaction mixture was conc in vacuo then the residue was dissolved inEtOAc and washed with H₂O, diluted NaHCO₃ solution and brine. Thesolution was dried (Na₂SO₄) and conc in vacuo. The residue was purifiedby chromatography with 0-10% MeOH—CH₂Cl₂ to give tert-butyl((R)-1-(((S)-1-(((6-amino-4-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(25 mg, 12% yield).

Step 2: To a solution of tert-butyl((R)-1-(((S)-1-(((6-amino-4-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(25 mg, 0.05 mol) in MeOH (2 mL) was added a solution of HCl-CPME (3 M,4 mL). The mixture was stirred for 2 h then cone in vacuo. The residuewas dissolved in MeOH and cone in vacuo then partitioned between H₂O andCH₂Cl₂. The H₂O layer was washed with CH₂Cl₂ and the volatiles removedin vacuo. The aqueous solution was lyophilized to give(R)-2-amino-N—((S)-1-(((6-amino-4-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride as a white powder (22.8 mg, 97% yield; 85:15diastereomer mixture).

Example 47. Preparation of(R)-2-Amino-N—((S)-1-(((6-amino-5-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1244)

(R)-2-Amino-N—((S)-1-(((6-amino-5-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized according to the procedures for compound(1243).

Example 48. Preparation of(R)-2-Amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1245)

tert-Butyl((R)-1-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas synthesized according to the procedure for compound (1243), step 1,except that additional HBTU (0.34 eq.) was added after stirring for 3.5h over ice bath. Following purification of the intermediate,deprotection was achieved according to the procedure for compound(1243), step 2.

Example 49. Preparation of(R)-2-Amino-N—((S)-1-((5-chloro-2-nitrobenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideHydrochloride (1246)

Step 1: tert-Butyl((R)-1-(((S)-1-((5-chloro-2-nitrobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatesynthesized according to step 1 of the procedure for compound (1242)using the appropriate starting materials.

Step 2: To tert-butyl((R)-1-(((S)-1-((5-chloro-2-nitrobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(12 mg, 0.025 mmol) was added conc HCl in MeOH (1 mL). The reactionmixture was allowed to stir at ambient temperature overnight, thenevaporated to dryness. The residue was taken up in H₂O-ACN (˜1:1) andlyophilized overnight to yield(R)-2-amino-N—((S)-1-((5-chloro-2-nitrobenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide,hydrochloride as a yellow powder (8.3 mg, 73%).

Example 50. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamideDihydrochloride (1247)

Step 1: To a stirred solution of 1-(tert-butyl) 2-methyl(R)-4-oxopyrrolidine-1,2-dicarboxylate (1.50 g, 6.16 mmol) in THF (15mL) at −78° C. was slowly added lithium bis(trimethylsilyl)amide (7.40mL, 7.40 mmol, 1 M in THF) under Ar. After stirring for 1 h at −78° C.,Comins' reagent (2.99 g, 7.40 mmol) in THF (5 mL) was added and thestirring continued for an additional 1 h. The reaction mixture wasstirred at −20° C. for additional 18 h. The reaction mixture wasquenched with 20 mL water and extracted with diethyl ether (3×60 mL).The combined extracts were washed with 2 N NaOH solution, dried overNa₂SO₄, filtered and concentrated under vacuum. The residue was purifiedby chromatography (EtOAc-hexanes) to give 1-(tert-butyl) 2-methyl(R)-4-(((trifluoromethyl)sulfonyl)oxy)-2,5-dihydro-1H-pyrrole-1,2-dicarboxylate(1.85 g, 80% yield).

Step 2: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 1-(tert-butyl) 2-methyl(R)-4-(((trifluoromethyl)sulfonyl)oxy)-2,5-dihydro-1H-pyrrole-1,2-dicarboxylate(400 mg, 1.06 mmol), m-tolyl boronic acid (215 mg, 1.17), Pd(PPh₃)₄(123mg, 0.11 mmol), K₂CO₃ (442 mg, 3.20 mmol), dioxane (7.1 mL) and water(1.5 mL). The resulting mixture was degassed by bubbling N₂ through thesolution for 10 min. The reaction was then heated to 80° C. for 2 h.Upon cooling to ambient temperature, the reaction solution was filteredthrough diatomaceous earth, eluting with EtOAc, concentrated andpurified by chromatography using EtOAc-hexanes to afford 1-(tert-butyl)2-methyl (R)-4-(m-tolyl)-2,5-dihydro-1H-pyrrole-1,2-dicarboxylate (330mg, 86% yield) as a colorless solid.

Step 3: To a stirred solution of 1-(tert-butyl) 2-methyl(R)-4-(m-tolyl)-2,5-dihydro-1H-pyrrole-1,2-dicarboxylate (317 mg, 1mmol) in THF (24 mL), MeOH (12 mL), and water (12 mL) was added LiOH(360 mg, 15 mmol) at ambient temperature. The resulting reaction mixturewas stirred at ambient temperature overnight. 12 mL of 1 M HCl was addedto the reaction mixture and organic volatiles were removed under vacuum.The aqueous layer was extracted with EtOAc (3×20 mL). The combinedorganic extracts were thoroughly dried using Na₂SO₄, filtered, andconcentrated to afford(R)-1-(tert-butoxycarbonyl)-4-(m-tolyl)-2,5-dihydro-1H-pyrrole-2-carboxylicacid (288 mg crude, 95% yield) that was directly used in the next stepwithout further purification.

Step 4: A solution of(R)-1-(tert-butoxycarbonyl)-4-(m-tolyl)-2,5-dihydro-1H-pyrrole-2-carboxylicacid (288 mg, 0.95 mmol) in MeOH (8 mL) was bubbled with Ar gas for 5min. 10% Pd/C (28 mg) was added to the reaction mixture and that wasstirred under 1 atm of H₂ for 4 h. The reaction mixture was filtered(0.2 μm syringe filter) and the filtrate was concentrated under vacuumto give(2R,4S)-1-(tert-butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carboxylic acid(265 mg, 92% yield).

Step 5: tert-Butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(404 mg, 74% yield) was synthesized from(2R,4S)-1-(tert-butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carboxylic acid(360 mg, 1.18 mmol) according to the procedure for compound (1304), step7.

Step 6:(2R,4S)-1-(tert-Butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carbonyl)-L-alanine(300 mg, 92% yield) was synthesized from tert-butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(404 mg, 0.87 mmol) according to the procedure for compound (1304), step4.

Step 7: tert-Butyl(2R,4S)-2-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(154 mg, 75% yield) was synthesized from(2R,4S)-1-(tert-butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carbonyl)-L-alanine(100 mg, 0.26 mmol) according to the procedure for compound (1234), step3.

Step 8: Benzyl(imino(4-(((S)-2-((2R,4S)-4-(m-tolyl)pyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamatedihydrochloride (83 mg, 90% yield) was synthesized from tert-butyl(2R,4S)-2-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(110 mg, 0.17 mmol) according to the procedure for compound (1304), step8.

Step 9:(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamidedihydrochloride (64 mg, 86%) was synthesized from benzyl(imino(4-(((S)-2-((2R,4S)-4-(m-tolyl)pyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(55 mg, 0.15 mmol) according to the procedure for compound (1304), step4.

Example 51. Preparation of(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)piperidine-2-carboxamideDihydrochloride (1248)

(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)piperidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1241). The first UVActive material eluting from the column in step 6was carried forward.

Example 52. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)piperidine-2-carboxamideDihydrochloride (1249)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound (1231) (9). Thethird UVActive material eluting from the column in step 6 was carriedforward.

Example 53. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-(4-(methylsulfonyl)piperazin-1-yl)benzyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1250)

Step 1: To a solution of 4-(piperazin-1-yl)benzaldehyde (450.0 mg, 2.37mmol) in THF (6 mL) and CH₂Cl₂ (6 mL), di-tert-butyl dicarbonate (650mg, 2.98 mmol) was added. After purging with N₂, the reaction wasstirred at room temp for 16 h. The reaction was quenched with 50 mL sat.NH₄Cl solution and extracted with 50 mL CH₂Cl₂ (3 times). The organiclayers were combined, dried (Na₂SO₄), vacuum filtered, and evaporatedunder vacuum. The crude product was dissolved in CH₂Cl₂ and adsorbed onsilica gel. Purification by chromatography (0-100% EtOAc-hexanes)afforded tert-butyl 4-(4-formylphenyl)piperazine-1-carboxylate (632.6mg, 92% yield).

Step 2: tert-Butyl4-(4-((((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)methyl)phenyl)piperazine-1-carboxylatewas synthesized according to the procedure for compound 1130, step 2.

Step 3: tert-Butyl4-(4-((((benzyloxy)carbonyl)((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)methyl)phenyl)piperazine-1-carboxylatewas synthesized according to the procedure for compound 1148, step 1.

Step 4: Deprotection of tert-butyl4-(4-((((benzyloxy)carbonyl)((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)methyl)phenyl)piperazine-1-carboxylatewas conducted according to the procedure for compound 1015, step 4except the crude product was purified by chromatography (5% 7 N NH₃ inMeOH—CH₂Cl₂) to afford benzyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)(4-(piperazin-1-yl)benzyl)carbamate.

Step 5: To a solution of benzyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)(4-(piperazin-1-yl)benzyl)carbamate(54.4 mg, 0.066 mmol) in DCE (500 μL) and TEA (14 μL) was added MsCl (6μL) at 0° C. The reaction was warmed to room temp and stirred for 16 h.The reaction was quenched with 1 mL 0.5 M NaOH solution and extractedwith 20 mL CH₂Cl₂ (3 times). The organic layers were combined, washedwith brine, dried (Na₂SO₄), vacuum filtered, and evaporated undervacuum. The crude product was dissolved in CH₂Cl₂ and adsorbed on silicagel. Purification by chromatography (0-10% MeOH—CH₂Cl₂) afforded benzyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)(4-(4-(methylsulfonyl)piperazin-1-yl)benzyl)carbamate.

Step 6: Deprotection of benzyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)(4-(4-(methylsulfonyl)piperazin-1-yl)benzyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-(4-(methylsulfonyl)piperazin-1-yl)benzyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 54. Preparation of(R)-2-amino-N—((S)-1-((4-carbamimidoyl-2-methoxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate salt (1251)

Step 1: A dry round bottom flask was charged with4-(hydroxymethyl)-3-methoxybenzonitrile (950 mg, 5.8 mmol), CBr₄ (2.12g, 6.4 mmol) and CH₂Cl₂ (20 mL), then cooled to 0° C. PPh₃ (1.68 g, 6.4mmol) was added and the reaction mixture stirred for 2 h at ambienttemperature. Upon completion, the reaction mixture was concentrated andthen purified by chromatography (40% EtOAc-hexanes) to furnish4-(bromomethyl)-3-methoxybenzonitrile as a white powder (1.1 g, 85%yield).

Step 2: In a dry round bottom flask under Ar, NaH (60% in mineral oil;508 mg, 12.7 mmol) was washed 3× with hexanes. Anhyd THF was added andthe suspension cooled to 0° C. A solution of4-(bromomethyl)-3-methoxybenzonitrile (1.1 g, 4.88 mmol) was addedfollowed by dropwise addition of di-tert-butyl-iminodicarboxylate (1.38g, 6.36 mmol) in THF. Reaction mixture was stirred for 16 h at ambienttemperature then quenched with H₂O. THF was removed in vacuo and theaqueous layer filtered through a fritted funnel. The crude product wasrecrystallized with hot EtOAc to furnish tert-butyl(tert-butoxycarbonyl)(4-cyano-2-methoxybenzyl)carbamate as a whitecrystalline solid (1.11 g, 63% yield).

Step 3: A 100 mL round bottom flask was charged with tert-butyl(tert-butoxycarbonyl)(4-cyano-2-methoxybenzyl)carbamate (1.11 g, 3.07mmol) and anhyd MeOH (10 mL), followed by hydroxylamine hydrochloride(1.07 g, 15.3 mmol) and DIEA (2.67 mL, 15.3 mmol). The reaction flaskwas equipped with a condenser and heated at reflux for 3 h. Uponcooling, the reaction mixture was then concentrated and the productprecipitated with H₂O. Crude product was collected by suctionfiltration, dissolved in CH₂Cl₂, washed with brine and dried overNa₂SO₄. Organic layers were collected and concentrated to furnishtert-butyl(E)-(tert-butoxycarbonyl)(4-(N′-hydroxycarbamimidoyl)-2-methoxybenzyl)carbamateas a white powder (1.12 g, 93% yield)

Step 4: A 100 mL round bottom flask was charged with(E)-(tert-butoxycarbonyl)(4-(N′-hydroxycarbamimidoyl)-2-methoxybenzyl)carbamate(1.12 g, 2.83 mmol), Ac₂O (320 μL, 3.35 mmol) and AcOH (5 mL). The flaskwas evacuated and backfilled with Ar then charged with 10% Pd/C (cat.).The flask was again evacuated and backfilled with H₂ and allowed to stirat ambient temperature for 16 h. Reaction mixture was filtered through a0.2 μm syringe filter and concentrated in vacuo to give tert-butyl(tert-butoxycarbonyl)(4-carbamimidoyl-2-methoxybenzyl)carbamate as awhite solid (1.25 g, quant.)

Step 5: To a solution of(tert-butoxycarbonyl)(4-carbamimidoyl-2-methoxybenzyl)carbamate (1.25 g,2.83 mmol) in THF (7 mL) was added sat. aq NaHCO₃ (7 mL) andN-(benzyloxycarbonyloxy)succinimide (741 mg, 3 mmol). The reactionmixture was stirred at ambient temperature for 16 h then diluted withEtOAc and washed with brine. The organic layer was dried over MgSO₄ andconcentrated. The residue was then triturated with diethyl ether toprovide tert-butyl(4-(N-((benzyloxy)carbonyl)carbamimidoyl)-2-methoxybenzyl)(tert-butoxycarbonyl)carbamateas a white powder (704 mg, 48% yield).

Step 6: tert-Butyl(4-(N-((benzyloxy)carbonyl)carbamimidoyl)-2-methoxybenzyl)(tert-butoxycarbonyl)carbamate(103 mg, 0.2 mmol) was deprotected according to the procedure forcompound 1015, step 4 to provide benzyl((4-(aminomethyl)-3-methoxyphenyl)(imino)methyl)carbamate hydrochlorideas a mint-green powder (68 mg, 97% yield).

Steps 7-8: Benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)-3-methoxyphenyl)(imino)methyl)carbamatewas synthesized according to steps 1-2 of the procedure for compound(1246) using the appropriate starting materials except the crudematerial was carried on without purification to the following step.

Step 9: Removal of the Cbz group of benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)-3-methoxyphenyl)(imino)methyl)carbamatewas carried out according to the procedure for compound 1028, step 6.The crude product was purified by reverse-phase HPLC (35-65%MeCN-H₂O+TFA) and the fractions lyophilized to furnish the titlecompound as a white powder.

Example 55. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)pyrrolidine-2-carboxamideDihydrochloride (1252)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(p-tolyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 56. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1253)

Step 1: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-4-(4-(trifluoromethyl)phenyl)butanoyl)-L-alanine(100 mg, 0.266 mmol) in CH₂Cl₂ (5 mL) was added NHS (1.1 equiv, 1.05mmol) with stirring at room temp. until dissolved. DCC (1.1 equiv, 1.05mmol) was added and stirred for 1.0 h then5-(aminomethyl)-6-methylpyridin-2-amine (0.319 mmol, 1.2 equiv.) wasadded with sonication and stirred overnight at room temp. The solutionwas filtered and evaporated to dryness. Flash chromatography (3% 7 N NH₃in MeOH/CH₂Cl₂) gave tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(91 mg, 69%) as a white solid.

Step 2: To tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(84 mg, 0.169 mmol) was added a solution of MeOH—HCl (5.0 mL, 227 mgHCl/mL) with stirring at room temp while monitoring for the consumptionof starting material. The solution was evaporated to dryness and MeOH(15 mL) was added and evaporated to dryness giving(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideas a white solid (80 mg, 100% yield).

Example 57. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamideHydrochloride (1254)

Step 1:(2R,4S)-1-(tert-Butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carbonyl)-L-alaninewas synthesized from 1-(tert-butyl) 2-methyl(R)-4-oxopyrrolidine-1,2-dicarboxylate according to the procedure forcompound (1247), step 1 to step 6.

Step 2: tert-Butyl(2R,4S)-2-(((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(57 mg, 70% yield) was synthesized from(2R,4S)-1-(tert-butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carbonyl)-L-alanine(60 mg, 0.16 mmol) according to the procedure for compound (1234), step3.

Step 3:(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamidehydrochloride (50.7 mg, 90% yield) was synthesized from tert-butyl(2R,4S)-2-(((S)-1-((5-chloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(m-tolyl)pyrrolidine-1-carboxylate(57 mg, 0.11 mmol) according to the procedure for compound (1304), step8.

Example 58. Preparation of(2R,4S)—N—((S)-1-(((6-Aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1255)

Step 1: To a solution of(2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carboxylic acid (1g, 3.4 mmol) in MeCN (25 mL) was added EDC (0.786 g, 4.1 mmol), HOBt(0.553 g, 4.1 mmol) and DIEA (3 mL, 17 mmol). The mixture was stirred atambient temperature for 15 min then benzyl L-alanine hydrochloride(0.884 g, 4.1 mmol) was added. The mixture was stirred overnight thencone in vacuo. The residue was dissolved in EtOAc and washed with 0.5 MKHSO₄, sat. NaHCO₃ 3×, brine and H₂O, dried (Na₂SO₄) and conc in vacuo.Purification by chromatography (5-40% EtOAc-hexanes) gave((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(1.05 g, 70% yield).

Step 2: To a degassed solution of((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(1.05 g, 2.3 mmol) in anhyd MeOH (20 mL) was added 10% Pd/C (0.30 g).The mixture was degassed then put under H₂ atm. After stirring overnightat ambient temperature, the mixture was filtered (0.20 μm syringefilter) then conc in vacuo to give 0.825 g of((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewhich was used without further purification (0.825 g, 98% yield).

Step 3:((2R,4S)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to 5-(aminomethyl)pyridin-2-amine according to the procedurefor compound (1243), step 1 to give tert-butyl(2R,4S)-2-(((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(150 mg, 73% yield).

Step 4: tert-Butyl(2R,4S)-2-(((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure for compound (1243), step 2except that 5-6 N HCl-IPA was used to give(2R,4S)—N—((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (127 mg, 90% yield).

Example 59. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(((6-hydroxynaphthalen-2-yl)methyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1256)

Step 1: Benzyl((4-(((S)-2-((R)-2-(((6-hydroxynaphthalen-2-yl)methyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-(((6-hydroxynaphthalen-2-yl)methyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(((6-hydroxynaphthalen-2-yl)methyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 60. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamideDihydrochloride (1257)

Step 1:(2R,4S)-1-(tert-Butoxycarbonyl)-4-(m-tolyl)pyrrolidine-2-carboxylic acidwas synthesized from 1-(tert-butyl) 2-methyl(R)-4-oxopyrrolidine-1,2-dicarboxylate according to the procedures forcompound (1247), step 1 to step 4.

Step 2:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), step 7 to step 8.

Example 61. Preparation of Methyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1258)

Step 1: To a 0° C. solution of tert-butyl(4-carbamimidoylbenzyl)carbamate acetate salt (100 mg, 0.32 mmol) inCH₂Cl₂ (8 mL, 0.04 M) was added DIEA (0.23 mL, 1.3 mmol), DMAP (6.3 mg,0.05 mmol), and methyl chloroformate (0.03 mL, 0.36 mmol). Afterstirring for 16 h at room temp, the reaction was quenched by addition ofsat. aq NaHCO₃. The resulting mixture was extracted with CH₂Cl₂, driedover anhyd Na₂SO₄, and conc under vacuum. The residue was purified bychromatography (0-100% EtOAc-hexanes) to give methyl((4-(((tert-butoxycarbonyl)amino)methyl)phenyl)(imino)methyl)carbamate(57 mg, 57% yield) as a white solid.

Step 2: Deprotection of ((4-(((tert-butoxycarbonyl)amino)methyl)phenyl)(imino)methyl)carbamate (121 mg, 0.39 mmol) was conducted according tothe procedure for compound (1259), step 2 to give methyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(125 mg, 100% yield).

Step 3: Methyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (230 mg, 0.72 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-((4-(N-(methoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(200 mg, 61% yield).

Step 4: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-((4-(N-(methoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(172 mg, 0.31 mmol) was conducted according to the procedure forcompound (1259), step 4 to give methyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(98 mg, 70% yield).

Example 62. Preparation of Benzyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1259)

Step 1: To a solution of tert-butyl (4-carbamimidoylbenzyl)carbamateacetate salt (100 mg, 0.32 mmol) in DMF (3 mL, 0.1 M) was added DIEA(0.23 mL, 1.3 mmol) and benzyl chloroformate (30% in toluene, 0.31 mL,0.65 mmol). After stirring for 16 h at room temperature, H₂O was addedand the solvents were removed under vacuum. The residue was partitionedwith EtOAc and H₂O. The organic layer was separated and washed with sat.aq NH₄Cl, H₂O, NaHCO₃. The organic layer was dried over anhyd Na₂SO₄ andcone under vacuum. The residue was purified by chromatography (50-100%EtOAc-hexanes) to give benzyl((4-(((tert-butoxycarbonyl)amino)methyl)phenyl)(imino)methyl)carbamate(77 mg, 62% yield) as a white solid.

Step 2: To a 0° C. solution of benzyl((4-(((tert-butoxycarbonyl)amino)methyl)phenyl)(imino)methyl)carbamate(66 mg, 0.17 mmol) in CH₂Cl₂ (1.5 mL, 0.1 M) was added 20% TFA in CH₂Cl₂(1.5 mL). After stirring for 2 h at room temperature, the reactionmixture was concentrated to give benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(48 mg, 100% yield).

Step 3: To a solution of((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(93 mg, 0.26 mmol) in CH₂Cl₂ (5 mL, 0.05 M) was added NHS (33 mg, 0.28mmol) with stirring at room temp until dissolved. DCC (59 mg, 0.28 mmol)was added and stirred for 1 h. The mixture was poured into a separatoryfunnel containing sat. aq NaHCO₃ (5 mL) and benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(123 mg, 0.31 mmol) and then shaken for 15 min. The organic layer wasfiltered through over a bed of anhyd Na₂SO₄ and evaporated to dryness.The residue was purified by chromatography (50-100% EtOAc-hexanes) togive tert-butyl(2R,4R)-2-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(128 mg, 79% yield).

Step 4: To a suspension of tert-butyl(2R,4R)-2-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(128 mg, 0.2 mmol) in methanol (2 mL, 0.1 M), was added a solution ofHCl/MeOH (2 mL, 227 mg HCl/mL). After stirring for 4 h at roomtemperature, the reaction mixture was concentrated. The residue waspurified by chromatography (0-100% [5% 7 N NH₃ in MeOH/CH₂Cl₂]—CH₂Cl₂)to give benzyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(60 mg, 56% yield).

Example 63. Preparation of Hexyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1260)

Step 1: To a 0° C. solution of tert-butyl(4-carbamimidoylbenzyl)carbamate acetate salt (200 mg, 0.65 mmol) inCH₂Cl₂ (8 mL, 0.08 M) was added DIEA (0.23 mL, 1.3 mmol). After stirringfor 15 min at the same temperature, hexyl chloroformate (0.13 mL, 0.78mmol) was added dropwise. After stirring for 1 h at the sametemperature, the reaction was quenched by addition of H₂O. The resultingmixture was extracted with CH₂Cl₂, dried over anhyd Na₂SO₄, and concunder vacuum. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give tert-butyl(4-(N-((hexyloxy)carbonyl)carbamimidoyl)benzyl)carbamate (151 mg, 62%yield).

Step 2: Deprotection of tert-butyl(4-(N-((hexyloxy)carbonyl)carbamimidoyl)benzyl)carbamate (150 mg, 0.4mmol) was conducted according to the procedure for compound (1259), step2 to give hexyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (155 mg, 100% yield).

Step 3: Hexyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (140 mg, 0.39 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-((4-(N-((hexyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(230 mg, 96% yield).

Step 4: To a 0° C. solution of tert-butyl(2R,4R)-2-(((S)-1-((4-(N-((hexyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(230 mg, 0.37 mmol) in CH₂Cl₂ (3.5 mL, 0.11 M) was added 20% TFA inCH₂Cl₂ (3.5 mL). After stirring for 3 h at room temp, the reactionmixture was concentrated. The residue was purified by chromatography(0-100% [5% 7 N NH₃ in MeOH/CH₂Cl₂]—CH₂Cl₂) to give hexyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(131 mg, 68% yield).

Example 64. Preparation of (R,E)-2-Amino-N—((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-phenylpent-4-enamideDihydrochloride (1261)

Step 1: To a solution of (R, E)-2-amino-5-phenylpent-4-enoic acid (0.97g, 5.07 mmol) in THF (15 mL), di-tert-butyl dicarbonate (1.1 g, 5.04mmol) was added followed by a solution of NaHCO₃ (1.2 g, 14.3 mmol) inH₂O (15 mL). The reaction mixture was cooled briefly over an ice bathand stirred for 1.5 h. Additional THF (10 mL) and sat. NaHCO₃ (1 mL)were added. The mixture was stirred overnight then EtOAc was added andthe mixture acidified with 0.5 M KHSO₄. The layers were separated, theaq layer was saturated with NaCl and extracted twice with EtOAc. Thecombined organics were washed with brine, dried (Na₂SO₄) and conc invacuo to give (R, E)-2-((tert-butoxycarbonyl)amino)-5-phenylpent-4-enoicacid (1.53 g, quant. yield).

Step 2: To a solution of (R,E)-2-((tert-butoxycarbonyl)amino)-5-phenylpent-4-enoic acid (1.53 g,5.25 mmol) in anhyd MeCN (27 mL) under Ar was added DIEA (2.0 mL, 11.5mmol). EDC (1.1 g, 5.7 mmol) and HOBt (0.79 g, 5.8 mmol) were added andthe mixture was stirred for 35 min. Methyl L-alaninate hydrochloride(0.89 g, 6.4 mmol) was added and the reaction stirred overnight. Themixture was conc in vacuo and the residue was dissolved in EtOAc, washedwith 0.5 M KHSO₄ 2×, H₂O, then sat NaHCO₃. The solution was dried(Na₂SO₄), conc in vacuo and purified by chromatography (0-35%EtOAc-hexanes) to give a sticky solid which was dissolved in MeCN—H₂Oand lyophilized. 1.3 g Of methyl((R,E)-2-((tert-butoxycarbonyl)amino)-5-phenylpent-4-enoyl)-L-alaninatewas isolated (66% yield).

Step 3: Methyl((R,E)-2-((tert-butoxycarbonyl)amino)-5-phenylpent-4-enoyl)-L-alaninatewas hydrolyzed according to the procedure for compound 1058 to give((R,E)-2-((tert-butoxycarbonyl)amino)-5-phenylpent-4-enoyl)-L-alanine(484 mg, quant. yield).

Step 4:((R,E)-2-((tert-Butoxycarbonyl)amino)-5-phenylpent-4-enoyl)-L-alaninewas coupled to 5-(aminomethyl)pyridin-2-amine according to the procedurefor compound (1243), step 1 to give tert-butyl((R,E)-1-(((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-5-phenylpent-4-en-2-yl)carbamate(116 mg, 91% yield).

Step 5: tert-Butyl((R,E)-1-(((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-5-phenylpent-4-en-2-yl)carbamatewas deprotected according to the procedure for compound (1255) to give(R,E)-2-amino-N—((S)-1-(((6-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-phenylpent-4-enamidedihydrochloride (101 mg, 93% yield).

Example 65. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-methoxyphenyl)pyrrolidine-2-carboxamideDihydrochloride (1262)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-methoxyphenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 66. Preparation of Propyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1263)

Step 1: tert-Butyl (4-(N-(propoxycarbonyl)carbamimidoyl)benzyl)carbamate(108 mg, 50% yield) was synthesized from tert-butyl(4-carbamimidoylbenzyl)carbamate acetate salt (198 mg, 0.64 mmol) andpropyl chloroformate according to the procedure for compound (1260),step 1.

Step 2: Deprotection of tert-butyl(4-(N-(propoxycarbonyl)carbamimidoyl)benzyl)-carbamate (108 mg, 0.32mmol) was conducted according to the procedure for compound (1259), step2 to give propyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (112 mg, 100% yield).

Step 3: Propyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (125 mg, 0.32 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-oxo-1-((4-(N-(propoxycarbonyl)carbamimidoyl)benzyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(176 mg, 95% yield).

Step 4: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-oxo-1-((4-(N-(propoxycarbonyl)carbamimidoyl)benzyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(176 mg, 0.3 mmol) was conducted according to the procedure for compound(1260), step 4 to give propyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(89 mg, 62% yield).

Example 67. Preparation of(2R,4R)—N—((S)-1-((4-((Z)—N′-Acetoxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(1264)

Step 1: To a solution of(2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carboxylic acid(1.0 g, 3.43 mmol) in MeCN (70 mL, 0.05 M) was added HOBt (577 mg, 3.77mmol), DIEA (2.39 mL, 13.7 mmol), and EDC (585 mg, 3.77 mmol). Afterstirring for 30 min at room temperature, benzyl L-alanine hydrochloride(814 mg, 3.77 mmol) was added and stirred for 16 h. The reaction mixturewas conc and the residue was partitioned with EtOAc and 10% KHSO₄solution. The organic layer was separated and washed with H₂O and sat.aq NaHCO₃. The organic layer was dried over anhyd Na₂SO₄ and conc undervacuum to give the crude tert-butyl(2R,4R)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(1.33 g, 86% yield) which was used in the next step without furtherpurification.

Step 2: A solution of the crude tert-butyl(2R,4R)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(1.55 g, 3.42 mmol) was degassed with a stream of Ar for 2 min. 10% Pd/C(70 mg) was added and a vacuum was pulled for 1 min. A balloon of H₂ wasadded and the reaction was monitored for the consumption of startingmaterial for 1.5 h. The catalyst was removed by filtration and thesolution was evaporated to give((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(1.24 g, 100% yield).

Step 3: To a solution of((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(1.16 g, 3.2 mmol) in CH₂Cl₂ (50 mL, 0.06 M) was added NHS (405 mg, 3.52mmol) with stirring at room temp until dissolved. DCC (726 mg, 3.52mmol) was added and stirred for 1 h. The mixture was poured into aseparatory funnel containing sat. aq NaHCO₃ (50 mL) and4-(aminomethyl)benzonitrile hydrochloride (647 mg, 3.84 mmol) and thenshaken for 15 min. The organic layer was filtered through over a bed ofanhyd Na₂SO₄ and evaporated to dryness. The residue was purified bychromatography (50-100% EtOAc-hexanes) to give tert-butyl(2R,4R)-2-(((S)-1-((4-cyanobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(1.3 g, 85% yield) as a white solid.

Step 4: To a solution of tert-butyl(2R,4R)-2-(((S)-1-((4-cyanobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(870 mg, 1.83 mmol) in MeOH (20 mL, 0.09 mmol) was added hydroxylaminehydrochloride (507 mg, 7.3 mmol) and DIEA (1.27 mL, 7.3 mmol). Afterstirring for 4 h at reflux, the reaction mixture was evaporated todryness. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give tert-butyl(2R,4R)-2-(((S)-1-((4-((Z)—N′-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(670 mg, 72% yield).

Step 5: To a suspension of tert-butyl(2R,4R)-2-(((S)-1-((4-((Z)—N-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(239 mg, 0.47 mmol) in acetic acid (5 mL) was added acetic anhydride (1mL). After stirring for 17 h at room temperature, the reaction mixturewas concd. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give tert-butyl(2R,4R)-2-(((S)-1-((4-((Z)—N-acetoxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(180 mg, 70% yield).

Step 6: A solution of tert-butyl(2R,4R)-2-(((S)-1-((4-((Z)—N-acetoxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(180 mg, 0.33 mmol) in EtOAc (1.5 mL) and CH₂Cl₂ (1.5 mL) was cooled inan ice bath. Hydrogen chloride was bubbled through the solution forapproximately 1 min. White foam was isolated by filtration and purifiedby chromatography (0-100% 5% 7 N NH3 in MeOH/CH₂Cl₂—CH₂Cl₂) to give(2R,4R)—N—((S)-1-((4-((Z)—N-acetoxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(62 mg, 42% yield).

Example 68. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1265)

Step 1: To a solution of((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(93 mg, 0.26 mmol, prepared according to the procedure for compound(1255) in CH₂Cl₂ (5 mL) was added NHS (33 mg, 0.28 mmol). The mixturewas stirred for 70 min then DCC was added. After stirring for 70 min,5-(aminomethyl)-6-methylpyridin-2-amine (47 mg, 0.34 mmol) was added.The mixture was stirred for 3 h then conc in vacuo to a smaller volume,filtered through a cotton plug and rinsed with 5% EtOAC-CH₂Cl₂. Thefiltrate was conc in vacuo then purified by chromatography (0-10%MeOH—CH₂Cl₂) to give tert-butyl(2R,4R)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(93 mg, 75% yield).

Step 2: tert-Butyl(2R,4R)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure for compound (1255). Thelyophilized solid was dissolved in MeOH, treated with Darco® charcoal(10 mg), warmed, then cooled to ambient temperature and filtered (0.20μm syringe filter). The filtrate was conc in vacuo to give(2R,4R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(81.8 mg, 93% yield).

Example 69. Preparation of(R)-2-Amino-N—((S)-1-(((6-amino-5-methoxypyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1266)

(R)-2-Amino-N—((S)-1-(((6-amino-5-methoxypyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized according to the procedure for compound(1243).

Example 70. Preparation of(R)-2-amino-N—((S)-1-(((6-amino-5-fluoropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1267)

(R)-2-Amino-N—((S)-1-(((6-amino-5-fluoropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized according to the procedure for compound(1243).

Example 71. Preparation of4-((((R)-1-(((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)methyl)benzamideDi-trifluoroacetate salt 1268)

Step 1: Benzyl((4-(((S)-2-((R)-2-((4-carbamoylbenzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-carbamoylbenzyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded4-((((R)-1-(((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)amino)methyl)benzamidedi-trifluoroacetate salt.

Example 72. Preparation of(2R,4R)—N—((S)-1-((2-Acetamido-5-chlorobenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1269)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-((2-amino-5-chlorobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas synthesized according to the procedure for compound 1119, step 3using the appropriate starting materials.

Steps 2-3: tert-Butyl(2R,4R)-2-(((S)-1-((2-amino-5-chlorobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(30 mg, 0.06 mmol) was dissolved in CH₂Cl₂ (1 mL) and treated with Ac₂O(28 μL, 0.3 mmol) and Et₃N (42 p L, 0.06 mmol) then stirred for 6 h atambient temperature. The reaction mixture was diluted with CH₂Cl₂ andwashed with 10% aq KHSO₄, brine and sat. aq NaHCO₃. The organic layerwas dried over Na₂SO₄ and concentrated, then the residue purified bychromatography (80-95% EtOAc-hexanes) to furnish tert-butyl(2R,4R)-2-(((S)-1-((2-acetamido-5-chlorobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylateas a colorless oil. Removal of the Boc protecting group was achievedupon treatment with 3 M HCl in iPrOH overnight at ambient temperature.Removal of iPrOH and lyophilization in a mixture of 1:1 ACN/H₂O gave thetitle compound as a white powder (15.9 mg, 52% yield over 2 steps).

Example 73. Preparation of(R)-2-Amino-N—((S)-1-(((6-carbamimidoylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate salt (1270)

(R)-2-Amino-N—((S)-1-(((6-carbamimidoylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound 1119 except using benzyl((5-(aminomethyl)pyridin-2-yl)(imino)methyl)carbamate (PCT Int. Appl.,2001087854, 22 Nov. 2001) in step 3. Purification was achieved by usingthe procedure for compound 1032.

Example 74. Preparation of(2R,4S)—N—((S)-1-(benzylamino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1271)

(2R,4S)—N—((S)-1-(Benzylamino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidewas synthesized according to the procedures for compound (1230), exceptusing benzyl amine in step 3.

Example 75. Preparation of(2R,4R)—N—((S)-1-(((6-Carbamimidoylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate (1272)

(2R,4R)—N—((S)-1-(((6-Carbamimidoylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound 1119 except using(2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carboxylic acid instep 1 and benzyl ((5-(aminomethyl)pyridin-2-yl)(imino)methyl)carbamatein step 3. Purification was achieved by using the procedure for compound1032.

Example 76. Preparation of5-(((S)-2-((2R,4R)-4-Phenylpyrrolidine-2-carboxamido)propanamido)methyl)picolinamideDihydrochloride (1273)

5-(((S)-2-((2R,4R)-4-Phenylpyrrolidine-2-carboxamido)propanamido)methyl)picolinamidewas isolated as a byproduct in the synthesis of (1272).

Example 77. Preparation of(2R,4R)—N—((S)-1-((5-chloro-2-(methylsulfonamido)benzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide,hydrochloride (1274)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-((2-amino-5-chlorobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(30 mg, 0.06 mmol) (as synthesize in Step 1 for compound (1269)) wasdissolved in CH₂Cl₂ (1 mL) and treated with MsCl (7 μL, 0.09 mmol) andEt₃N (25 μL, 0.18 mmol), then stirred for 16 h at ambient temperature.The reaction mixture was diluted with CH₂Cl₂ and washed with 10% aqKHSO₄, brine and sat. aq NaHCO₃. The organic layer was dried over Na₂SO₄and concentrated, then the residue purified by chromatography (80-90%EtOAc/hexanes) to furnish tert-butyl(2R,4R)-2-(((S)-1-((5-chloro-2-(methylsulfonamido)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylateas a colorless oil. Removal of the Boc protecting group was achievedupon treatment with 3 M HCl in iPrOH overnight at ambient temperature.Removal of iPrOH and lyophilization in a mixture of 1:1 ACN/H₂O gave thetitle compound as a pink-tinged fluffy solid (1.9 mg, 6% yield over 2steps).

Example 78. Preparation of(R)-2-Amino-N—((S)-1-(((6-amino-5-chloropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1275)

(R)-2-Amino-N—((S)-1-(((6-amino-5-chloropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized according to the procedure for compound(1243).

Example 79. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-(trifluoromethyl)phenyl)pyrrolidine-2-carboxamideDihydrochloride (1276)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-(trifluoromethyl)phenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 80. Preparation of(2R,4S)-4-(3-(Aminomethyl)phenyl)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideTrihydrochloride (1277)

(2R,4S)-4-(3-(Aminomethyl)phenyl)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidetrihydrochloride was synthesized according to the procedures forcompound (1247).

Example 81. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-cyanophenyl)pyrrolidine-2-carboxamideDihydrochloride (1278)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-cyanophenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 82. Preparation of(R)-2-amino-N—((S)-1-((5-bromo-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide,hydrochloride (1279)

Steps 1-2:(R)-2-amino-N—((S)-1-((5-bromo-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide,hydrochloride was synthesized as a white fluffy powder according tosteps 1-2 of the procedure for compound (1246) using the appropriatestarting materials (31.4 mg, 44% yield over two steps).

Example 83. Preparation of(R)-2-Amino-N—((S)-1-(((6-(aminomethyl)pyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1280)

Step 1: To a suspension of 6-(aminomethyl)nicotinonitrile (2.05 g, 9.95mmol) in THF (50 mL) was added sat. NaHCO₃ (50 mL). The mixture wasstirred 30 min then benzyl chloroformate (1.6 mL, 11.3 mmol) was added.After stirring vigorously for 2 h, the mixture was diluted with EtOAcand the layers were separated. The aqueous layer was extracted withEtOAc and the combined organics were washed with brine, dried (Na₂SO₄)and conc in vacuo. The crude material was crystallized from warmhexanes-Et₂O. The solid was collected by filtration, rinsed withEt₂O-hexanes and -10% EtOAc-hexanes and air dried to give benzyl((5-cyanopyridin-2-yl)methyl)carbamate (805 mg, 30% yield).

Step 2: To a solution of benzyl ((5-cyanopyridin-2-yl)methyl)carbamate(0.80 g, 2.99 mmol) in MeOH (50 mL) was added NiCl₂ (0.43 g, 3.29 mmol)and di-tert-butyl dicarbonate (2.05 g, 9.4 mmol). The mixture was cooledover an ice bath and NaBH₄ (0.445 g, 11.8 mmol) was added in twoaliquots over 10 min. The reaction was allowed to warm to ambienttemperature, stirred overnight, then conc in vacuo. The residue wasdissolved in EtOAc and 0.5 M KHSO₄. The layers were separated, and theaqueous layer was adjusted to pH 10 with sat. NaHCO₃ and 2 M NaOH. Afterextraction with EtOAc, the combined organics were washed with H₂O anddilute aqueous NH₄OH solution containing brine. The solution was dried(Na₂SO₄) and conc in vacuo. Purification by chromatography (10-80%EtOAc-hexanes) provided benzyl((5-(((tert-butoxycarbonyl)amino)methyl)pyridin-2-yl)methyl)carbamate(527 mg, 47% yield).

Step 3: To a solution of benzyl((5-(((tert-butoxycarbonyl)amino)methyl)pyridin-2-yl)methyl)carbamate(527 mg, 1.42 mmol) in MeOH (10 mL) was added 3 M HCl-CPME (10 mL).After stirring for 3 h, EtOAc was added to the slurry. The solid wascollected by filtration, rinsed with EtOAc and hexanes and dried to givebenzyl ((5-(aminomethyl)pyridin-2-yl)methyl)carbamate dihydrochloride(412 mg, 94% yield).

Step 4: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alanine (122 mg,0.35 mmol) and NHS (44 mg, 0.38 mmol) in CH₂Cl₂ (8 mL) was added DCC (77mg, 0.37 mmol) and the mixture was stirred for 1 h. In a separate vial,benzyl ((5-(aminomethyl)pyridin-2-yl)methyl)carbamate dihydrochloride(140 mg, 0.45 mmol) was treated with CH₂Cl₂ (2 mL) and sat. NaHCO₃ (2.5mL). This biphasic mixture was added to the reaction and stirred for 70min. The layers were separated then the organic layers washed with H₂Oand brine, then dried (Na₂SO₄) and cone in vacuo. Purification bychromatography (50-100%) EtOAc gave tert-butyl((R)-1-(((S)-1-(((6-((((benzyloxy)carbonyl)amino)methyl)pyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(113 mg, 54% yield).

Step 5: tert-Butyl((R)-1-(((S)-1-(((6-((((benzyloxy)carbonyl)amino)methyl)pyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas deprotected with 3 M HCl-CPME according to the procedure for (1315),except that the reaction mixture was conc in vacuo to give benzyl((5-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)pyridin-2-yl)methyl)carbamatedihydrochloride.

Step 6: To a degassed solution benzyl((5-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)pyridin-2-yl)methyl)carbamatefrom the previous step in MeOH (8 mL) was added 10% Pd/C (18 mg). Themixture was placed under H₂ atm and stirred at ambient temperatureovernight. After degassing the mixture, 1 M HCl (0.5 mL) was added thenthe slurry was filtered (0.2 μm syringe filter) and conc in vacuo. Theresidue was dissolved in H₂O, washed with CH₂Cl₂ 3×then conc in vacuo.Dissolution of the residue in EtOAc-MeOH followed by cone in vacuo gave(R)-2-amino-N—((S)-1-(((6-(aminomethyl)pyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride as an off-white solid (88 mg, quant. yield).

Example 84. Preparation of(2R,4R)—N-((2S)-1-(((2-Amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1281)

Step 1: To a 25-mL round bottom flask, commercially availableN-((4-oxocyclohexyl)methyl)acetamide (467.0 mg, 2.76 mmol) was added andfollowed by CH₂Cl₂ (5 mL). After purging with N₂, a solution of Br₂ (140μL, 2.73 mmol) in CH₂Cl₂ (10 mL) was added dropwise at room temp by asyringe pump at the rate of 0.317 mL per min. After the addition, thereaction was heated to reflux for 1 h. Volatiles was evaporated undervacuum to afford the crude N-((3-bromo-4-oxocyclohexyl)methyl)acetamide.

Step 2: To a 25-mL round bottom flask, the crudeN-((3-bromo-4-oxocyclohexyl)methyl)acetamide was added and followed byEtOH (8 mL) and thiourea at room temp. After purging with N₂, thereaction was heated to reflux for 2 h. Volatiles was evaporated undervacuum. The crude product was diluted with water (10 mL) and followed byslow addition of 1M NaOH solution to become basic (pH about 13). Thebasic solution was extracted with 15 mL EtOAc (3 times). The organiclayers were combined, washed with brine, dried (Na₂SO₄), vacuumfiltered, and evaporated under vacuum. The crude product was dissolvedin CH₂Cl₂ and adsorbed on silica gel. Purification by chromatography(0-15% MeOH—CH₂Cl₂) gaveN-((2-amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)methyl)acetamide(48.5 mg, 8% yield).

Step 3: To a 25-mL round bottom flask,N-((2-amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)methyl)acetamide(48.5 mg, 0.213 mmol) was added and followed by the addition ofcommercially available aqueous HBr solution (2 mL, 48% in water). Afterpurging with N₂, the reaction was heated to reflux for 18 h. Volatileswas evaporated under vacuum to afford crude6-(aminomethyl)-4,5,6,7-tetrahydrobenzo[d]thiazol-2-amine dihydrobromidesalt.

Step 4:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(69.0 mg, 0.190 mmol) was coupled with the crude6-(aminomethyl)-4,5,6,7-tetrahydrobenzo[d]thiazol-2-amine dihydrobromideaccording to the procedure for compound 1116, step 1 to affordtert-butyl(2R,4R)-2-(((2S)-1-(((2-amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(64.1 mg, 64% yield).

Step 5: Deprotection of tert-butyl(2R,4R)-2-(((2S)-1-(((2-amino-4,5,6,7-tetrahydrobenzo[d]thiazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(64.1 mg, 0.121 mmol) was done according to the procedure for compound1119, step 2. Purification by reverse phase HPLC (5-45-75-90% MeCN—H₂O)afforded(2R,4R)—N-((2S)-1-(((2-amino-4,5,6,7-tetrahydrobenzo[d]′thiazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedi-trifluoroacetate salt (16.0 mg, 31% yield).

Example 85. Preparation of(2S,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamideDihydrochloride (1282)

(2S,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), steps 7 and 8 starting from commercially available(2S,4R)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid.

Example 86. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamideDihydrochloride (1283)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), steps 7 and 8 starting from commercially available(2R,4R)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid.

Example 87. Preparation of(2R,4R)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1284)

(2R,4R)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1247), except that the final product was purified usingreverse-phase HPLC.

Example 88. Preparation of(2S,4R)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDihydrochloride (1285)

(2S,4R)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 89. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylthiazole-2-carboxamideHydrochloride (1286)

(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylthiazole-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1234), except that a few drops of conc HCl was added to the reactionmixture during the benzyl carbamate deprotection step.

Example 90. Preparation of(R)-2-amino-N—((S)-1-((5-Chloro-2-(hydroxymethyl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideHydrochloride (1287)

Steps 1-2: The title compound was synthesized as a white powderaccording to steps 1-2 of the procedure for compound (1246) using theappropriate starting materials (27.5 mg, 31% yield over two steps).

Example 91. Preparation of 2,2,2-Trichloroethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1288)

Step 1: To a 0° C. solution of tert-butyl(4-carbamimidoylbenzyl)carbamate acetate salt (100 mg, 0.32 mmol) in DMF(2 mL, 0.16 M) was added trichloroethyl chloroformate (0.09 mL, 0.65mmol) and Et₃N (0.18 mL, 1.29 mmol). After stirring for 1 h at the sametemperature, the reaction was quenched by addition of H₂O. The resultingmixture was extracted with EtOAc, dried over anhyd Na₂SO₄, and concunder vacuum. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give tert-butyl(4-(N-((2,2,2-trichloroethoxy)carbonyl)carbamimidoyl)benzyl)carbamate(82 mg, 60% yield).

Step 2: Deprotection of tert-butyl(4-(N-((2,2,2-trichloroethoxy)carbonyl)carbamimidoyl)benzyl)carbamate(165 mg, 0.39 mmol) was conducted according to the procedure forcompound (1259), step 2 to give 2,2,2-trichloroethyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(126 mg, 100% yield).

Step 3: 2,2,2-Trichloroethyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(170 mg, 0.39 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to give2,2,2-trichloroethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(180 mg, 83% yield).

Step 4: Deprotection of(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(180 mg, 0.27 mmol) was conducted according to the procedure forcompound (1260), step 4 to give 2,2,2-trichloroethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(112 mg, 73% yield).

Example 92. Preparation of(R)-2-Amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxobutan-2-yl)-4-phenylbutanamideDihydrochloride (1289)

(R)-2-Amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxobutan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized using(S)-2-((tert-butoxycarbonyl)amino)butanoic acid in step 1 according tothe procedures for compound 1050.

Example 93. Preparation of(2R,4R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxobutan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1290)

(2R,4R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxobutan-2-yl)-4-phenylpyrrolidine-2-carboxamidewas synthesized using (S)-2-((tert-butoxycarbonyl)amino)butanoic acid instep 1 and(2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carboxylic acid instep 3 according to the procedures for compound 1050.

Example 94. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(aminomethyl)phenyl)pyrrolidine-2-carboxamideDihydrochloride (1291)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(aminomethyl)phenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1257).

Example 95. Preparation of(R)—N-(4-((Z)—N′-Hydroxycarbamimidoyl)benzyl)-2-methyl-4-oxo-4-((2R,4R)-4-phenylpyrrolidin-2-yl)butanamide(1292)

Deprotection of tert-butyl(2R,4R)-2-(((S)-1-((4-((Z)—N′-hydroxycarbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(173 mg, 0.34 mmol) was conducted according to the procedure forcompound (1260), step 4 to give(R)—N-(4-((Z)—N′-hydroxycarbamimidoyl)benzyl)-2-methyl-4-oxo-4-((2R,4R)-4-phenylpyrrolidin-2-yl)butanamide(103 mg, 71% yield).

Example 96. Preparation of Isobutyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1293)

Step 1: tert-Butyl(4-(N-(isobutoxycarbonyl)carbamimidoyl)benzyl)carbamate (145 mg, 64%yield) was synthesized from tert-butyl (4-carbamimidoylbenzyl)carbamateacetate salt (200 mg, 0.65 mmol) and isobutyl chloroformate according tothe procedure for compound (1288), step 1.

Step 2: Deprotection of tert-butyl(4-(N-(isobutoxycarbonyl)carbamimidoyl)benzyl)carbamate (145 mg, 0.42mmol) was conducted according to the procedure for compound (1259), step2 to give isobutyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (150 mg, 100% yield).

Step 3: Isobutyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (150 mg, 0.42 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-((4-(N-(isobutoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(173 mg, 84% yield).

Step 4: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-((4-(N-(isobutoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(173 mg, 0.29 mmol) was conducted according to the procedure forcompound (1260), step 4 to give isobutyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(111 mg, 77% yield).

Example 97. Preparation of Ethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1294)

Step 1: tert-Butyl (4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)carbamate(142 mg, 68% yield) was synthesized from tert-butyl(4-carbamimidoylbenzyl)carbamate acetic acid (200 mg, 0.65 mmol) andethyl chloroformate according to the procedure for compound (1288), step1.

Step 2: Deprotection of tert-butyl(4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)carbamate (142 mg, 0.44 mmol)was conducted according to the procedure compound (1259), step 2 to giveethyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetatesalt (148 mg, 100% yield).

Step 3: Ethyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamatetrifluoroacetate salt (130 mg, 0.39 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-((4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(168 mg, 91% yield).

Step 4: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-((4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(168 mg, 0.3 mmol) was conducted according to the procedure for compound(1260), step 4 to give ethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(102 mg, 74% yield).

Example 98. Preparation of(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-3-phenyl-1H-pyrazole-5-carboxamide(1295)

(S)—N-(1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-3-phenyl-1H-pyrazole-5-carboxamidewas synthesized according to the procedures for compound (1234).

Example 99. Preparation of(R)-2-Amino-N—((S)-1-(((2-aminopyridin-4-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1296)

Step 1: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninewas coupled with 4-(aminomethyl)pyridin-2-amine according to theprocedure for compound (1265) step 1, except that a small amount of sat.NaHCO₃ was added to the reaction mixture. Following extractive workup,purification by chromatography (0-10% MeOH—CH₂Cl₂) gave tert-butyl((R)-1-(((S)-1-(((2-aminopyridin-4-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(90 mg, 57% yield).

Step 2: tert-Butyl((R)-1-(((S)-1-(((2-aminopyridin-4-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas deprotected according to the procedure for compound (1243) to give(R)-2-amino-N—((S)-1-(((2-aminopyridin-4-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride (85 mg, quant. yield).

Example 100. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperidine-2-carboxamideDihydrochloride (1297)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1231) (9) (the third UVActive material eluting from the column in step6 was carried forward) and compound (1253) steps 1 and 2.

Example 101. Preparation of(2R,4R)—N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1298)

Step 1: A 100 mL round bottom flask was charged with AcOH (18 mL) andH₂SO₄ (2 mL), then cooled to 0° C. Cl—N-(hydroxymethyl)acetamide (4.32g, 35 mmol) and 4-chloro-2-methylphenol (5 g, 35 mmol) were addedportionwise to the stirring acidic solution, then the reaction mixtureallowed to warm to ambient temperature overnight. The reaction mixturewas poured into ice-cold H₂O then extracted with CH₂Cl₂×3. Combinedorganic layers were washed with brine, dried over Na₂SO₄ andconcentrated to produce a colorless oil. The intermediate was dissolvedin EtOH (10 mL), treated with conc. HCl (3 mL) and refluxed for 2 h. Theresulting yellow suspension was then stored at −10° C. overnight andfiltered with EtOH to yield 2-(aminomethyl)-4-chloro-6-methylphenol,hydrochloride as a white fluffy solid (1.67 g, 23% yield).

Steps 2-3: The title compound was synthesized as a white powderaccording to steps 1-2 of the procedure for compound (1246) using theappropriate starting materials (36.7 mg, 25% yield over two steps).

Example 102. Preparation of(R)-2-Amino-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideHydrochloride (1299)

Steps 1-2: The title compound was synthesized as a white granular solidaccording to steps 1-2 of the procedure for compound (1246) using theappropriate starting materials (65 mg, 59% yield over two steps).

Example 103. Preparation of(2R,4R)—N—((S)-1-((4-Carbamimidoyl-3-fluorobenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1300)

Step 1: To a solution of 4-(aminomethyl)-2-fluorobenzonitrile (986.0 mg,6.57 mmol) in MeCN (5.5 mL) was added DIEA (1.2 mL, 6.89 mmol) anddi-tert-butyl dicarbonate (1.44 g, 6.60 mmol) at room temp. Afterpurging with N₂, the reaction was stirred at room temp for 16 h.Volatiles was evaporated under vacuum. The crude product was dilutedwith EtOAc (200 mL) and washed with 10% KHSO₄ solution (100 mL, 2times). The organic layer was washed with brine, dried (Na₂SO₄), vacuumfiltered, and evaporated under vacuum. The crude product was dissolvedin CH₂Cl₂ and adsorbed on silica gel. Purification by chromatography(0-15% MeOH—CH₂Cl₂) afforded tert-butyl(4-cyano-3-fluorobenzyl)carbamate (1.19g, 73% yield).

Step 2: Benzyl ((4-(aminomethyl)-2-fluorophenyl)(imino)methyl)carbamatehydrochloride was synthesized according to the procedure for compound1251, steps 3-6.

Step 3: Benzyl((2-fluoro-4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound (1281), steps4-5.

Step 4: Deprotection of benzyl((2-fluoro-4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75-90% MeCN—H₂O) afforded(2R,4R)—N—((S)-1-((4-carbamimidoyl-3-fluorobenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedi-trifluoroacetate salt.

Example 104. Preparation of(2R,4R)—N—((S)-1-(((5-Chloro-2-oxo-1,2-dihydropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1301)

(2R,4R)—N—((S)-1-(((5-Chloro-2-oxo-1,2-dihydropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedure given forcompound (1296).

Example 105. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-ethylphenyl)pyrrolidine-2-carboxamideDihydrochloride (1302)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-ethylphenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 106. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-ethylphenyl)pyrrolidine-2-carboxamideDihydrochloride (1303)

The first four steps to synthesize(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-ethylphenyl)pyrrolidine-2-carboxamidedihydrochloride was performed according to the procedures for compound(1257).

Example 107. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamideDihydrochloride (1304)

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (1.50 g, 4.70 mmol) in THF (31mL) at −78° C. was slowly added lithium bis(trimethylsilyl)amide (5.17mL, 5.17 mmol, 1 M in THF) under Ar atmosphere. After stirring for 1 hat −78° C., benzyl bromide (0.653 mL, 5.65 mmol) was added and thestirring continued for an additional 2 h. The reaction mixture wasquenched with sat. NH₄Cl solution and extracted with diethyl ether (3×60mL). The combined extracts were dried over Na₂SO₄, filtered andconcentrated under vacuum. The residue was purified by chromatography(EtOAc-hexanes) gave 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzyl-5-oxopyrrolidine-1,2-dicarboxylate (1.60 g, 83% yield).

Step 2: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzyl-5-oxopyrrolidine-1,2-dicarboxylate (1.60 g, 3.91 mmol)in THF (26 mL) at −78° C. was added lithium triethylborohydride solution(4.30 mL, 4.30 mmol, 1 M in THF) under Ar atmosphere. After 30 min, thereaction mixture was quenched with sat. NaHCO₃ solution (8.60 mL) andwarmed to 0° C. At 0° C., 30% H₂O₂(about 25 drops) was added and thereaction mixture was stirred at same temperature for 30 min. The organicvolatiles were removed under vacuum and the aqueous layer was extractedwith CH₂Cl₂ (3×40 mL). The combined organic extracts were thoroughlydried using Na₂SO₄, filtered, concentrated to afford 2-benzyl1-(tert-butyl) (2R,4S)-4-benzyl-5-hydroxypyrrolidine-1,2-dicarboxylate(1.70 g crude) that was directly used in the next step without furtherpurification.

Step 3: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzyl-5-hydroxypyrrolidine-1,2-dicarboxylate (1.70 g crude)and triethylsilane (0.685 mL, 4.30 mmol) in CH₂Cl₂ (20 mL) at −78° C.was drop wise added boron trifluoride diethyl etherate (0.531 mL, 4.30mmol) under Ar atmosphere. After 30 min at same temperature additionaltriethylsilane (0.685 mL, 4.30 mmol) and boron trifluoride diethyletherate (0.531 mL, 4.30 mmol) were added. After stirring for 2 h at−78° C., the reaction mixture was quenched with sat. aqueous NaHCO₃solution (10 mL) and extracted with CH₂Cl₂(3×40 mL). The combinedextracts were dried over Na₂SO₄, filtered and conc under vacuum. Theresidue was purified by chromatography (EtOAc-hexanes) to afford2-benzyl 1-(tert-butyl) (2R,4S)-4-benzylpyrrolidine-1,2-dicarboxylate(1.00 g, 65% yield in two steps).

Step 4: A solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzylpyrrolidine-1, 2-dicarboxylate (1.00 g, 2.53 mmol) inMeOH (20 mL) was bubbled with Ar gas for 5 minutes. 10% Pd/C (100 mg)was added to the reaction mixture and that was stirred under 1atmosphere of H₂ for 3 h. The reaction mixture was filtered (0.2 μMsyringe filter) and the filtrate was concentrated under vacuum to give(2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid(700 mg, 91% yield).

Step 5: To a stirred solution of (tert-butoxycarbonyl)-L-alanine (1.96g, 10.38 mmol) in CH₂Cl₂ (55 mL) was added NHS (1.25 g, 10.89 mmol) atroom temperature. To the reaction mixture DCC (2.25 g 10.9 mmol) wasadded and the reaction mixture stirred for 1.0 h.5-(Aminomethyl)-6-methylpyridin-2-amine was added to the reactionmixture and sonicated for 5 min. The5-(aminomethyl)-6-methylpyridin-2-amine was completely dissolved andstirred the reaction mixture at ambient temperature for 1 h. The crudereaction mixture was filtered and conc under reduced pressure. The crudereaction mixture was purified by chromatography (MeOH/CH₂Cl₂) to affordtert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 70% yield) as a white solid.

Step 6: To tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 7.62 mmol) was added a solution of MeOH—HCl (19 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (typically 1 h). The solution was evaporated todryness and MeOH (50 mL) was added and evaporated to dryness to removeresidual HCl gas to give(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (1.60 g, 90% yield) as an off white solid (hygroscopic).

Step 7: To a stirred solution of(2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid(100 mg, 0.33 mmol) in anhydrous DMF (3.3 mL) was added HOBt (50 mg,0.36 mmol), DIEA (0.23 mL, 1.32 mmol) and EDC (69 mg, 0.36 mmol) atambient temperature. The reaction mixture was stirred for 30 min atambient temperature.(S)-2-Amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (97 mg, 0.396 mmol) was added to the reaction mixture andstirred overnight. The solution was evaporated to dryness and theresidue was partitioned with EtOAc (20 mL) and 10% KHSO₄ (15 mL). Theorganic layer was separated and washed with sat. NaHCO₃ solution (20ml), dried over anhydrous Na₂SO₄ and conc under vacuum. The crudereaction mixture was purified by chromatography using MeOH—CH₂Cl₂ toafford tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(124 mg, 76% yield) as a white solid.

Step 8: To tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(124 mg, 0.25 mmol) was added a solution of MeOH—HCl (2.0 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (30 min to 1h). The solution was evaporated to drynessand MeOH (10 mL) was added and evaporated to dryness to remove residualHCl gas to yield(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamidedihydrochloride (94 mg, 95% yield) as a white solid.

Example 108. Preparation of 2,2,2-Trifluoroethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(1305)

Step 1: tert-Butyl (4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)carbamate(139 mg, 57% yield) was synthesized from tert-butyl(4-carbamimidoylbenzyl)carbamate acetate salt (200 mg, 0.65 mmol) andtrifluoroethyl chloroformate according to the procedure for compound(1288), step 1.

Step 2: Deprotection of tert-butyl(4-(N-(ethoxycarbonyl)carbamimidoyl)benzyl)carbamate (139 mg, 0.37 mmol)was conducted according to the procedure for compound (1259), step 2 togive 2,2,2-trifluoroethyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(144 mg, 100% yield).

Step 3: 2,2,2-Trifluoroethyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate trifluoroacetate salt(144 mg, 0.37 mmol) was coupled with((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanineaccording to the procedure for compound (1259), step 3 to givetert-butyl(2R,4R)-2-(((S)-1-oxo-1-((4-(N-((2,2,2-trifluoroethoxy)carbonyl)carbamimidoyl)benzyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(168 mg, 88% yield).

Step 4: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-oxo-1-((4-(N-((2,2,2-trifluoroethoxy)carbonyl)carbamimidoyl)benzyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(168 mg, 0.27 mmol) was conducted according to the procedure forcompound (1260), step 4 to give 2,2,2-trifluoroethyl(imino(4-(((S)-2-((2R,4R)-4-phenylpyrrolidine-2-carboxamido)propanamido)methyl)phenyl)methyl)carbamate(60 mg, 43% yield).

Example 109. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDihydrochloride (1306)

(2R,4S)-4-Benzyl-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), step 1 to step 4 and compound (1247), step 5 to step 9.

Example 110. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1307)

Step 1: (2R,4S)-4-Benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid was synthesized from 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate according to the procedures forcompound (1304), step 1 to step 4.

Step 2: tert-Butyl(2R,4S)-4-benzyl-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(350 mg, 66% yield) was synthesized from(2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid(350 mg, 1.14 mmol) according to the procedures for compound (1304),step 7.

Step 3:((2R,4S)-4-Benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carbonyl)-L-alanine(254 mg, 90% yield) was synthesized from tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(350 mg, 0.75 mmol) according to the procedures for compound (1304),step 4.

Step 4: tert-Butyl(2R,4S)-4-benzyl-2-(((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(66 mg, 70% yield) was synthesized from((2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carbonyl)-L-alanine(67 mg, 0.18 mmol) according to the procedure for compound (1234), step3.

Step 5:(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidehydrochloride (41 mg, 80% yield) was synthesized from tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(66 mg, 0.12 mmol) according to the procedure for compound (1234), step3.

Example 111. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1308)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1253).

Example 112. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperazine-2-carboxamideDihydrochloride (1309)

Step 1: To a stirred solution of 1-(tert-butyl) 2-methyl(R)-piperazine-1,2-dicarboxylate (2.0 g. 8.2 mmol) in CH₂Cl₂ was addednaphthalen-1-ylboronic acid (9.8 mmol, 1.2 equiv) and Cu(OAc)₂ (500 mg)and stirring continued for 48 h under a balloon of air. The solution waswashed with H₂O, dried over Na₂SO₄ and evaporated. Column chromatography(20% EtOAc-hexanes) gave 1-(tert-butyl) 2-methyl(R)-4-(naphthalen-1-yl)piperazine-1,2-dicarboxylate (402 mg, 13% yield)as an oil.

Step 2: To a stirred solution of 1-(tert-butyl) 2-methyl(R)-4-(naphthalen-1-yl)piperazine-1,2-dicarboxylate (390 mg, 1.05 mmol)in MeOH—H₂O was added LiOH (3.15 mmol, 3.0 equiv.) with heating at 60°C. for 3 h. The solution is evaporated to dryness and H₂O was added withswirling. The pH was adjusted to 5 with 10% KHSO₄ and the product wascollected by filtration, washed with H₂O and dried.(R)-1-(Tert-butoxycarbonyl)-4-(naphthalen-1-yl)piperazine-2-carboxylicacid was isolated (335 mg, 89% yield) as a tan solid.

Step 3: tert-Butyl(R)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-(naphthalen-1-yl)piperazine-1-carboxylatewas synthesized according to the procedure for compound (1230).

Steps 4-6:(R)—N—((S)-5-(6-Amino-2-methylpyridin-3-yl)-3-oxopentan-2-yl)-4-(naphthalen-1-yl)piperazine-2-carboxamidewas synthesized according to the procedures for compound (1253).

Example 113. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenoxypyrrolidine-2-carboxamideDihydrochloride (1310)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenoxypyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 114. Preparation of(2R,4R)—N—((S)-1-(((1H-Pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1311)

Step 1:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to (1H-pyrrolo[2,3-b]pyridin-5-yl)methanamine according tothe procedure given for compound (1265), step 1. Purification bychromatography (0-10% MeOH—CH₂Cl₂) gave tert-butyl(2R,4R)-2-(((S)-1-(((1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(100 mg, 69% yield).

Step 2: tert-Butyl(2R,4R)-2-(((S)-1-(((1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure given for compound (1243) togive(2R,4R)—N—((S)-1-(((1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (89.9 mg, 95% yield).

Example 115. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1312)

Step 1: Benzyl((4-(((S)-2-((R)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-45-90% MeCN—H₂O) afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 116. Preparation of(2R,5S)-5-Amino-N-(5-chloro-2-cyanobenzyl)-2-methyl-4-oxo-7-phenylheptanamideTrifluoroacetate salt (1313)

Step 1: A dry 50 mL round bottom flask was charged with NaH (60% inmineral oil) (246 mg, 6.16 mmol) and washed with hexanes 3×under Ar. DryTHF (5 mL) was then added and the suspension cooled to 0° C.2-(Bromomethyl)-4-chlorobenzonitrile (650 mg, 2.8 mmol) was dissolved inTHF (5 mL) and added to the stirring suspension, followed bydi-tert-butyl-iminodicarboxylate (679 mg, 3.1 mmol) in THF (5 mL)dropwise. The reaction mixture was allowed to warm to ambienttemperature overnight, then quenched with H₂O, poured into sat. aq NH₄Cland extracted with EtOAc 2×. The combined organic layers were washedwith brine and dried over Na₂SO₄. The crude product was then loaded ontosilica gel and purified by chromatography (0-30% EtOAc/hexanes) to yieldboth di-tert-butyl (5-chloro-2-cyanobenzyl)iminodicarbonate (672 mg, 65%yield) and tert-butyl (5-chloro-2-cyanobenzyl)carbamate (158 mg, 21%yield).

Step 2: Di-tert-butyl (5-chloro-2-cyanobenzyl)iminodicarbonate (110 mg,0.3 mmol) was dissolved in CH₂Cl₂ and treated with TFA (300 μL) atambient temperature. After 2 hours, the reaction mixture wasconcentrated in vacuo to yield 2-(aminomethyl)-4-chlorobenzonitrile,trifluoroacetate as a white powder (79 mg, quant. yield).

Step 3: tert-Butyl((R)-1-(((S)-1-((5-chloro-2-cyanobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas synthesized according to step 1 of the procedure for compound (1246)using the appropriate starting materials.

Step 4: tert-Butyl((R)-1-(((S)-1-((5-chloro-2-cyanobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(120 mg, 0.24 mmol) was dissolved in CH₂Cl₂ (2 mL) and treated with TFA(˜500 μL). After stirring at ambient temperature overnight, the reactionmixture was concentrated, taken up in ACN/H₂O and lyophilized to yieldthe title compound as a white solid (17 mg, 14% yield over two steps).

Example 117. Preparation of(R)-2-Amino-N—((S)-1-((5-cyano-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideTrifluoroacetate salt (1314)

Steps 1-2: The title compound was synthesized as a white solid accordingto steps 3-4 of the procedure for compound (1313) using the appropriatestarting materials (17 mg, 17% yield over two steps).

Example 118. Preparation of(S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl(R)-2-amino-4-phenylbutanoate Hydrochloride (1315)

Step 1: To a stirred solution of(R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoic acid (838 mg, 3mmol)), benzyl (S)-lactate (507 μL, 3.15 mmol) and DMAP (403 mg, 3.3mmol) in CH₂Cl₂ (15 mL) was added DCC (681 mg, 3.3 mmol). The mixturewas stirred for 18 h, then diluted with CH₂Cl₂ and washed with 10% aqKHSO₄, brine and sat. aq. NaHCO₃. The organic layer was dried overNa₂SO₄ and concentrated in vacuo. Chromatography (20% EtOAc/hexanes)gave (S)-1-(benzyloxy)-1-oxopropan-2-yl(R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoate (1 g, 76% yield).

Step 2: Removal of the benzyl group of(S)-1-(benzyloxy)-1-oxopropan-2-yl(R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoate was carried outaccording to the procedure for compound 1028, step 6.

Steps 3-5: (S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl(R)-2-amino-4-phenylbutanoate hydrochloride was synthesized as a whitegranular solid according to steps 3-5 of the procedure for compound 1119using the appropriate starting materials.

Example 119. Preparation of(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-isopropylphenyl)pyrrolidine-2-carboxamideDihydrochloride (1316)

(2R,4S)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-isopropylphenyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 120. Preparation of(R)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperazine-2-carboxamideHydrochloride (1317)

(R)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperazine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1230), except using(R)-1-(tert-butoxycarbonyl)-4-(naphthalen-1-yl)piperazine-2-carboxylicacid in step 1 and 2-(aminomethyl)-4-chloro-6-methylphenol in step 3.

Example 121. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamideDihydrochloride (1318)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 122. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamideDihydrochloride salt (1319)

Step 1: (R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoic acid (5.0 g,17.9 mmol) was coupled with commercially available benzyl L-alaninatehydrochloride (4.8 g, 22.3 mmol) according to the procedure for compound1119, step 1 to afford benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninate (6.9g, 87% yield).

Step 2: Deprotection of benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninate (6.9g, 15.7 mmol)) according to the procedure for compound 1119, step 2afforded ((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alanine(5.3 g, 96% yield).

Step 3: ((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alanine(470.0 mg, 1.34 mmol) was coupled with commercially available5-(aminomethyl)-6-methylpyridin-2-amine (560.0 mg, 1.75 mmol) accordingto the procedure for compound 1088, step 2 except HBTU was added to thereaction at 0° C. afforded tert-butyl((R)-1-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(181.6 mg, 29% yield).

Step 4: Deprotection of tert-butyl((R)-1-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(181.6 mg, 0.387 mmol) according to the procedure for compound 1119,step 4 afforded(R)-2-amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(115.7 mg, 81% yield).

Step 5:(R)-2-Amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(115.7 mg, 0.313 mmol) was reacted with 3-(3-hydroxyphenyl)propanal(68.0 mg, 0.453 mmol) according to the procedure for compound 1130, step2. The crude product was dissolved in CH₂Cl₂ and adsorbed onto silicagel. Purification by chromatography (0-15% MeOH—CH₂Cl₂) afforded(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamide(42.3 mg, 27% yield).

Step 6: To a solution ofR)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamidein MeOH (1 mL) was added HCl in MeOH (0.5 mL, ca. 4 M). Volatile wasevaporated under vacuum to afford(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-(3-hydroxyphenyl)propyl)amino)-4-phenylbutanamidedihydrochloride salt.

Example 123. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-oxo-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1320)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-oxo-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304) except that the final product was purified usingreverse-phase HPLC.

Example 124. Preparation of(2R,4S)—N—((R)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-oxo-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1321)

(2R,4S)—N—((R)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-5-oxo-4-(3-(trifluoromethyl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), except that the final product was purified usingreverse-phase HPLC.

Example 125. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenethylpyrrolidine-2-carboxamideDihydrochloride (1322)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenethylpyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1247).

Example 126. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-ethylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1323)

Step 1: To a solution of tert-butyl(5-cyano-6-ethylpyridin-2-yl)carbamate (370 mg, 1.5 mmol; synthesizedaccording to U.S. Pat. No. 5,668,289) in MeOH (5 mL) was added 7 MNH₃-MeOH (25 mL). The solution was briefly degassed then Raney nickel(˜0.3 g) was added. The reaction was put under H₂ atm and stirred 5.5 h.After reduction was complete, part of the mixture was filtered throughdiatomaceous earth. The remainder was filtered through paper. Thecombined filtrates were conc in vacuo. The residue was dissolved in 5%H₂O-MeOH and filtered (0.2 μm syringe filter) then conc in vacuo to givetert-butyl (5-(aminomethyl)-6-ethylpyridin-2-yl)carbamate as a whitesolid (323 mg, 86% yield).

Step 2:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to tert-butyl (5-(aminomethyl)-6-ethylpyridin-2-yl)carbamateaccording to the procedure for compound (1265), step 1 to givetert-butyl(2R,4R)-2-(((S)-1-(((6-amino-2-ethylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(134 mg, 77% yield).

Step 3: tert-Butyl(2R,4R)-2-(((S)-1-(((6-amino-2-ethylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure given for compound (1243),except that the product was not extracted with CH₂Cl₂. The aqueoussolution was filtered (0.2 μm syringe filter) then lyophilized to give(2R,4R)—N—((S)-1-(((6-amino-2-ethylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (114.9 mg, quant. yield).

Example 127. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1324)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), except that the final product was purified usingreverse-phase HPLC.

Example 128. Preparation of(R)-2-amino-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(1325)

Steps 1-2: The title compound was synthesized as a white solid accordingto steps 3-4 of the procedure for compound (1313) using the appropriatestarting materials (42 mg, 38% yield over two steps).

Example 129. Preparation of(R)-2-Amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-3-(4-hydroxyphenyl)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate salt (1326)

Step 1: To a solution of Boc-D-homophenylalanine (300 mg, 1.07 mmol) inanhyd DMF (6 mL, 0.18 M) was added HOBt (214 mg, 1.4 mmol), DIEA (0.75mL, 4.3 mmol), and EDC (208 mg, 1.34 mmol). After stirring for 30 min atroom temperature, L-tyrosine methyl ester hydrochloride (354 mg, 1.29mmol) was added and stirred for 16 h. The reaction mixture was conc andthe residue was partitioned with EtOAc and 10% KHSO₄ solution. Theorganic layer was separated and washed with H₂O and sat. aq NaHCO₃. Theorganic layer was dried over anhyd Na₂SO₄ and concd. The residue waspurified by chromatography (0-100% EtOAc-hexanes) to give methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-tyrosinate (365mg, 74% yield).

Step 2: To a solution of methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-tyrosinate (365mg, 0.8 mmol) in THF (6 mL) and H₂O (6 mL) was added LiOH (38 mg, 1.6mmol). After stirring for 4 h at room temperature, the reaction mixturewas cone to remove THF. To the above mixture was added 10% KHSO₄solution, extracted with EtOAc, dried over anhyd Na₂SO₄, and conc undervacuum. The residue was purified by chromatography (0-100% [5% 7 N NH₃in MeOH/CH₂Cl₂]—CH₂Cl₂) to give((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-tyrosine (290mg, 82% yield).

Step 3: To a solution of((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-tyrosine (290mg, 0.65 mmol) in CH₂Cl₂ (18 mL, 0.04 M) was added NHS (83 mg, 0.72mmol) with stirring at room temp until dissolved. DCC (148 mg, 0.72mmol) was added and stirred for 1 h. Benzyl((4-(aminomethyl)phenyl)(imino)methyl)carbamate (222 mg, 0.78 mmol) wasadded to the above mixture and stirred for 1 h. The reaction wasquenched by addition of H₂O and the resulting mixture was extracted withCH₂Cl₂, dried over anhyd Na₂SO₄, and conc under vacuum. The residue waspurified by chromatography (0-100% EtOAc-hexanes) to give tert-butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-(4-hydroxyphenyl)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(244 mg, 52% yield).

Step 4: Deprotection of tert-butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-(4-hydroxyphenyl)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(244 mg, 0.34 mmol) was conducted according to the procedure forcompound (1260), step 4 to give benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)-3-(4-hydroxyphenyl)propanamido)methyl)phenyl)(imino)methyl)carbamate(126 mg, 61% yield).

Step 5: Deprotection of benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)-3-(4-hydroxyphenyl)propanamido)methyl)phenyl)(imino)methyl)carbamate(126 mg, 0.21 mmol) was conducted according to the procedure forcompound (1264), step 2 except that the crude material was purifiedusing reverse-phase HPLC.

Example 130. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-hydroxyphenethyl)amino)-4-phenylbutanamidedihydrochloride (1327)

Step 1: Benzyl ((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate (1.9 g, 41% yield in 4 steps) wassynthesized by a method similar to that used for compound 1119, exceptthe crude product was purified by chromatography(10% MeOH—CH₂Cl₂ andthen 5% 7 N NH₃ in MeOH—CH₂Cl₂).

Step 2: To a 25-mL round bottom flask, 4-(2-hydroxyethyl)phenol (1 g,7.24 mmol,) was added and followed by DMSO (8 mL). After purging withN₂, the reaction was treated with TEA (2.2 mL) and followed by theaddition of a solution of sulfur trioxide pyridine complex (2.50 g, 15.7mmol) in DMSO (9 mL) by cannulation. The reaction was stirred at roomtemp for 1 h and quenched with ice water. The reaction mixture wasdiluted with CH₂Cl₂ and washed with ice water (3 times). The organiclayer was collected, washed with brine, dried (Na₂SO₄), vacuum filtered,and evaporated under vacuum. The crude product was dissolved in CH₂Cl₂and adsorbed on silica gel. Purification by chromatography (0-100%EtOAc-hexanes) afforded 2-(4-hydroxyphenyl)acetaldehyde (227.4 mg, 23%yield).

Step 3: Benzyl ((4-(((S)-2-((R)-2-((4-hydroxyphenethyl)amino)-4phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamate wassynthesized according to the procedure for compound 1130, step 2.

Step 4: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-hydroxyphenethyl)amino)-4phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl) according tothe procedure for compound 1130, step 3 afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-hydroxyphenethyl)amino)-4-phenylbutanamide.

Step 5:(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-hydroxyphenethyl)amino)-4-phenylbutanamidedihydrochloride was formed according to the procedure for compound(1319), step 6.

Example 131. Preparation of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chlorobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1328)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chlorobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except that the benzyl deprotection was done by following LiOHconditions as shown below.

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chlorobenzyl)pyrrolidine-1,2-dicarboxylate (329 mg, 1 mmol)in THF (24 mL), MeOH (12 mL), and water (12 mL) was added LiOH (360 mg,15 mmol) at ambient temperature. The resulting reaction mixture wasstirred at ambient temperature overnight. Aqueous HCl (12 mL, 1 M) wasadded to the reaction mixture and organic volatiles were removed undervacuum. The aqueous layer was extracted with EtOAc (3×20 mL). Thecombined organic extracts were thoroughly dried using Na₂SO₄, filtered,and concentrated to afford(2R,4S)-1-(tert-butoxycarbonyl)-4-(3-chlorobenzyl)pyrrolidine-2-carboxylicacid (320 mg crude, 0.96 mmol) that was directly used in the next stepwithout further purification.

Example 132. Preparation of(2R,4R)—N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1329)

Step 1: To a solution of 1H-pyrrolo[2,3-b]pyridine-5-carbonitrile (1.04g, 7.24 mmol) in anhyd DMF (14 mL) under Ar was added NCS (1.06 g, 6.9mmol). The mixture was heated at 55° C. for 2.5 h, cooled to ambienttemperature, then diluted with H₂O until the final volume was −90 mL.The mixture was cooled and the solid was isolated by filtration, rinsedwith H₂O and dried in a vac oven (at ambient temperature) to give3-chloro-1H-pyrrolo[2,3-b]pyridine-5-carbonitrile (1.2 g, 93% yield).

Step 2: To a suspension of3-chloro-1H-pyrrolo[2,3-b]pyridine-5-carbonitrile (0.50 g, 2.8 mmol) inMeOH (75 mL) was added di-tert-butyl dicarbonate (1.29 g, 5.9 mmol) andCoCl₂-6H₂O (0.36 g, 1.5 mmol). NaBH₄ (0.37 g, 9.8 mmol) was added in 4aliquots over 20 min. The mixture was stirred for 2 h then additionalNaBH₄ (0.21 g, 5.6 mmol) was added and stirred overnight. The reactionwas acidified with 0.5 M KHSO₄ until the pH was neutral. Volatiles wereremoved in vacuo then the aqueous mixture was extracted with 10%MeOH—CH₂Cl₂ twice. The aqueous layer was re-adjusted to neutral pH andextracted with 10% MeOH—CH₂Cl₂. The combined organics were conc in vacuoto remove all volatiles and H₂O. Purification by chromatography (tworuns: with 0-5% MeOH—CH₂Cl₂ then 0-25% acetone-CH₂Cl₂) gave tert-butyl((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)carbamate (307 mg, 39%yield).

Step 3: To a suspension of tert-butyl((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)carbamate (305 mg, 1.08mmol) in MeOH (6 mL) was added 3 M HCl-CPME (9 mL). The resultingsolution was stirred for 2.5 h then additional 3 M HCl-CPME (5 mL) wasadded. After stirring for 45 min, the solution was cone in vacuo. Theresidue was dissolved in MeOH and cone in vacuo. The solid was suspendedin MeOH-Et₂O and the solid was collected by filtration and air dried togive (3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methanamine hydrochloride(285 mg, quant. yield).

Step 4:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to (3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methanamineaccording to the procedure for compound (1265) to give tert-butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(71.7 mg, 62% yield).

Step 5: tert-Butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure for compound (1243), exceptthat the reaction mixture was diluted with Et₂O. The solid was collectedby filtration, rinsed with 2% MeOH-Et₂O and dried in a vac ovenovernight to give(2R,4R)—N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (64 mg, 96% yield).

Example 133. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1330)

Step 1: 2-(3-Hydroxyphenyl)acetaldehyde was synthesized according to theprocedure for compound (1327), step 2.

Step 2: Benzyl((4-(((S)-2-((R)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 3: Deprotection of benzyl((4-(((S)-2-((R)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas done according to the procedure for compound 1130, step 3.Purification by reverse phase HPLC (5-75% MeCN—H₂O) afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 134. Preparation of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethylbenzyl)pyrrolidine-2-carboxamideDihydrochloride (1331)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethylbenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 135. Preparation of(R)-2-Amino-N—((S)-1-((4-carbamimidoylbenzyl)amino)-3-(1H-imidazol-5-yl)-1-oxopropan-2-yl)-4-phenylbutanamideDi-trifluoroacetate (1332)

Step 1: Methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-histidinate (500mg, 65% yield) was synthesized from Boc-D-homophenylalanine (500 mg,1.79 mmol) and L-histidine methyl ester dihydrochloride according to theprocedure for compound (1326), step 1.

Step 2:((R)-2-((tert-Butoxycarbonyl)amino)-4-phenylbutanoyl)-L-histidine (320mg, 66% yield) was synthesized from methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-histidinate (500mg, 1.16 mmol) according to the procedure for compound (1326), step 2.

Step 3: tert-Butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-(1H-imidazol-5-yl)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(160 mg, 30% yield) was synthesized from((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-histidine (320mg, 0.77 mmol) according to the procedure for compound (1326), step 3.

Step 4: Deprotection of tert-butyl((R)-1-(((S)-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-3-(1H-imidazol-5-yl)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(160 mg, 0.23 mmol) was conducted according to the procedure forcompound (1260), step 4 to give benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)-3-(1H-imidazol-5-yl)propanamido)methyl)phenyl)(imino)methyl)carbamate(49 mg, 36% yield).

Step 5: Deprotection of benzyl((4-(((S)-2-((R)-2-amino-4-phenylbutanamido)-3-(1H-imidazol-5-yl)propanamido)methyl)phenyl)(imino)methyl)carbamate(49 mg, 0.08 mmol) was conducted according to the procedure for compound(1264), step 2 except that the crude material was purified usingreverse-phase HPLC.

Example 136. Preparation of(2R,4R)—N—((S)-1-((3-Chloro-5-methylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1333)

Steps 1-2: The title compound was synthesized as a white powderaccording to steps 1-2 of the procedure for compound (1246) using theappropriate starting materials (46 mg, 53% yield over two steps).

Example 137. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-hydrochloride (1334)

Step 1: tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(46 mg, 80% yield) was synthesized from((2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carbonyl)-L-alanine(40 mg, 0.11 mmol) according to the procedure for compound (1234), step3.

Step 2:(2R,4S)-4-Benzyl-N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-hydrochloride (38.2 mg, 80% yield) was synthesized from tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(46 mg, 0.85 mmol) according to the procedure for compound (1234), step3.

Example 138. Preparation of(S)-2-((R)-2-Amino-4-phenylbutanamido)-N′-(4-carbamimidoylbenzyl)pentanediamideDi-trifluoroacetate (1335)

Step 1: Methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-glutaminate (149mg, 41% yield) was synthesized from Boc-D-homophenylalanine (241 mg,0.86 mmol) and L-glutamine methyl ester hydrochloride according to theprocedure for compound (1326), step 1.

Step 2: ((R)-2-Amino-4-phenylbutanoyl)-L-glutamine (112 mg, 78% yield)was synthesized from methyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-glutaminate (149mg, 0.35 mmol) according to the procedure for compound (1326), step 2except that the crude material was applied to the next step withoutfurther purification.

Step 3: tert-Butyl((R)-1-(((S)-5-amino-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1,5-dioxopentan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(156 mg, 84% yield) was synthesized from((R)-2-amino-4-phenylbutanoyl)-L-glutamine (112 mg, 0.28 mmol) accordingto the procedure for compound (1326), step 3.

Step 4: Deprotection of tert-butyl((R)-1-(((S)-5-amino-1-((4-(N-((benzyloxy)carbonyl)carbamimidoyl)benzyl)amino)-1,5-dioxopentan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(156 mg, 0.23 mmol) was conducted according to the procedure forcompound (1260), step 4 to give benzyl((4-(((S)-5-amino-2-((R)-2-amino-4-phenylbutanamido)-5-oxopentanamido)methyl)phenyl)(imino)methyl)carbamate(47 mg, 36% yield).

Step 5: Deprotection of benzyl((4-(((S)-5-amino-2-((R)-2-amino-4-phenylbutanamido)-5-oxopentanamido)methyl)phenyl)(imino)methyl)carbamate(47 mg, 0.08 mmol) was conducted according to the procedure for compound(1264), step 2 except that the crude material was purified usingreverse-phase HPLC.

Example 139. Preparation of(2R,4R)—N—((S)-1-(((3-Amino-1H-pyrazol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1336)

Step 1: 3-Amino-1H-pyrazole-5-carbonitrile was reduced according to theprocedure for compound (1311), step 1 to give5-(aminomethyl)-1H-pyrazol-3-amine which was used in the next stepwithout further purification.

Step 2:((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled with 5-(aminomethyl)-1H-pyrazol-3-amine following theprocedure given for compound (1265), step 1 except that the amine wasadded to the reaction mixture as a solution in DMF. After the reactionwas complete, the mixture was diluted with 5% MeOH—CH₂Cl₂ and washedwith sat. NaHCO₃ and brine, dried (Na₂SO₄) and conc in vacuo.Purification by chromatography (0-10% MeOH—CH₂Cl₂) provided tert-butyl(2R,4R)-2-(((S)-1-(((3-amino-1H-pyrazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(64 mg, 47% yield).

Step 3: tert-Butyl(2R,4R)-2-(((S)-1-(((3-amino-1H-pyrazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure given for compound (1323),step 3 to give(2R,4R)—N—((S)-1-(((3-amino-1H-pyrazol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (60 mg, quant. yield).

Example 140. Preparation of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-methylbenzyl)pyrrolidine-2-carboxamidedihydrochloride (1337)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-methylbenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 141. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamideDihydrochloride (1338)

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (600 g, 1.88 mmol) in THF (12.5mL) at −78° C. was slowly added lithium bis(trimethylsilyl)amide (2.06mL, 2.06 mmol, 1 M in THF) under Ar atmosphere. After stirring for 1 hat −78° C., 2-(bromomethyl)naphthalene (500 mg, 2.26 mmol) in 1 mL THFwas added and the stirring continued for an additional 2 h. The reactionmixture was quenched with sat. NH₄Cl solution and extracted with diethylether (3×20 mL). The combined extracts were dried over Na₂SO₄ filteredand concentrated under vacuum. The residue was purified bychromatography (EtOAc-hexanes) gave 2-benzyl 1-(tert-butyl)(2R,4S)-4-(naphthalen-2-ylmethyl)-5-oxopyrrolidine-1,2-dicarboxylate(600 mg, 70% yield).

Step 2: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(naphthalen-2-ylmethyl)-5-oxopyrrolidine-1,2-dicarboxylate(600 mg, 3.91 mmol) in THF (8.6 mL) at −78° C. was added lithiumtriethylborohydride solution (1.56 mL, 1.56 mmol, 1 M in THF) under Aratmosphere. After 30 min, the reaction mixture was quenched with sat.NaHCO₃ solution (3 mL) and warmed to 0° C. At 0° C., 30% H₂O₂(about 10drops) was added and the reaction mixture was stirred at sametemperature for 30 min. The organic volatiles were removed under vacuumand the aqueous layer was extracted with CH₂Cl₂ (3×10 mL). The combinedorganic extracts were thoroughly dried using Na₂SO₄, filtered,concentrated to 2-benzyl 1-(tert-butyl)(2R,4S)-5-hydroxy-4-(naphthalen-2-ylmethyl)pyrrolidine-1,2-dicarboxylate(550 mg crude) that was directly used in the next step without furtherpurification.

Step 3: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4S)-5-hydroxy-4-(naphthalen-2-ylmethyl)pyrrolidine-1,2-dicarboxylate(550 mg crude) and triethylsilane (0.25 mL, 1.56 mmol) in CH₂Cl₂ (5.5mL) at −78° C. was drop wise added boron trifluoride diethyl etherate(0.19 mL, 1.56 mmol) under Ar. After 30 min at same temperatureadditional triethylsilane (0.25 mL, 1.56 mmol) and boron trifluoridediethyl etherate (0.19 mL, 1.56 mmol) were added. After stirring for 2 hat −78° C., the reaction mixture was quenched with sat. aqueous NaHCO₃solution (5 mL) and extracted with CH₂Cl₂ (3×15 mL). The combinedextracts were dried over Na₂SO₄ filtered and conc under vacuum. Theresidue was purified by chromatography (EtOAc-hexanes) to afford2-benzyl 1-(tert-butyl)(2R,4S)-4-(naphthalen-2-ylmethyl)pyrrolidine-1,2-dicarboxylate (350 mg,60% yield in two steps).

Step 4: A solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(naphthalen-2-ylmethyl)pyrrolidine-1,2-dicarboxylate (350 mg,0.78 mmol) in MeOH (8 mL) was bubbled with Ar gas for 5 minutes. 10%Pd/C (35 mg) was added to the reaction mixture and stirred under 1 atmof H₂ for 3 h. The reaction mixture was filtered (0.2 μM syringe filter)and the filtrate was concentrated under vacuum to give(2R,4S)-1-(tert-butoxycarbonyl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxylicacid (250 mg, 90% yield).

Step 5: To a stirred solution of (tert-butoxycarbonyl)-L-alanine (1.96g, 10.38 mmol) in CH₂Cl₂ (55 mL) was added NHS (1.25 g, 10.89 mmol) atroom temperature. To the reaction mixture DCC (2.25 g 10.9 mmol) wasadded and the reaction mixture stirred for 1.0 h.5-(Aminomethyl)-6-methylpyridin-2-amine was added to the reactionmixture and sonicated for 5 min. The5-(aminomethyl)-6-methylpyridin-2-amine was completely dissolved andstirred the reaction mixture at ambient temperature for 1 h. The crudereaction mixture was filtered and cone under reduced pressure.Purification by chromatography using MeOH—CH₂Cl₂ afforded tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 70% yield) as a white solid.

Step 6: To tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 7.62 mmol) was added a solution of MeOH—HCl (19 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (typically 1 h). The solution was evaporated todryness and MeOH (50 mL) was added and evaporated to dryness to removeresidual HCl gas to give(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (1.60 g, 90% yield) as an off white solid (Hygroscopic).

Step 7: To a stirred solution of(2R,4S)-1-(tert-butoxycarbonyl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxylicacid (75 mg, 0.21 mmol) in anhydrous DMF (1.4 mL) was added HOBt (32 mg,0.23 mmol), DIEA (0.15 mL, 0.84 mmol) and EDC (45 mg, 0.23 mmol) atambient temperature. The reaction mixture was stirred for 30 min atambient temperature.(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (61 mg, 0.32 mmol) was added to the reaction mixture andstirred overnight. The solution was evaporated to dryness and theresidue was partitioned with EtOAc (15 mL) and 10% KHSO₄ (10 mL). Theorganic layer was separated and washed with sat. NaHCO₃ solution (10mL), dried over anhydrous Na₂SO₄ and conc under vacuum. The crudereaction mixture was purified by chromatography using MeOH—CH₂Cl₂ toafford tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(naphthalen-2-ylmethyl)pyrrolidine-1-carboxylate(52 mg, 45% yield) as a white solid.

Step 8: To tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(naphthalen-2-ylmethyl)pyrrolidine-1-carboxylate(52 mg, 0.095 mmol) was added a solution of MeOH—HCl (2.0 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (30 min to 1h). The solution was evaporated to drynessand MeOH (10 mL) was added and evaporated to dryness to remove residualHCl gas to yield(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamidedihydrochloride (29 mg, 74% yield) as a white solid.

Example 142. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-chlorophenethyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1339)

Step 1: Benzyl((4-(((S)-2-((R)-2-((4-chlorophenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-chlorophenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatecarbamate according to the procedure for compound 1130, step 3.Purification by reverse phase HPLC (5-75% MeCN—H₂O) to afford(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-((4-chlorophenethyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 143. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(phenethylamino)-4-phenylbutanamideDihydrochloride (1340)

Step 1: Benzyl(imino(4-(((S)-2-((R)-2-(phenethylamino)-4-phenylbutanamido)propanamido)methyl)phenyl)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl(imino(4-(((S)-2-((R)-2-(phenethylamino)-4-phenylbutanamido)propanamido)methyl)phenyl)methyl)carbamateaccording to the procedure for compound 1130, step 3 afforded(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(phenethylamino)-4-phenylbutanamide.

Step 3:(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-2-(phenethylamino)-4-phenylbutanamidedihydrochloride was formed according to the procedure for compound(1319), step 6.

Example 144. Preparation of(R)-2-amino-N—((S)-1-((5-chloro-2-(1H-1,2,4-triazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(1341)

Steps 1-2: The title compound was synthesized as a white solid accordingto steps 3-4 of the procedure for compound (1313) using the appropriatestarting materials (36 mg, 32% yield over two steps).

Example 145. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperidine-2-carboxamideDihydrochloride (1342)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-yl)piperidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1231) (the first UVActive material eluting from the column in step 6was carried forward) and compound (1253), steps 1 and 2.

Example 146. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(isoquinolin-5-ylmethyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1343)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(isoquinolin-5-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), except that the final product was purified usingreverse-phase HPLC.

Example 147. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((±)-1-phenylethyl)pyrrolidine-2-carboxamideDihydrochloride (1344)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((±)-1-phenylethyl)pyrrolidine-2-carboxamidedihydrochloride was followed according to the procedures for compound(1257).

Example 148. Preparation of(R)-2-((4-acetamidophenethyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride (1345)

Step 1: Benzyl((4-(((S)-2-((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl((4-(((S)-2-((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanamido)propanamido)methyl)phenyl)(imino)methyl)according to the procedure for compound 1130, step 3 afforded(R)-2-((4-acetamidophenethyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide.

Step 3:(R)-2-((4-Acetamidophenethyl)amino)-N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was formed according to the procedure for compound(1319), step 6.

Example 149. Preparation of(R)-2-Amino-N—((S)-1-(((2-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1346)

(R)-2-Amino-N—((S)-1-(((2-aminopyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was synthesized according to the procedures given forcompound (1323), steps 2 and 3.

Example 150. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperazine-2-carboxamideDihydrochloride (1347)

(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperazine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1253).

Example 151. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2-methylbenzyl)piperazine-2-carboxamideDihydrochloride (1348)

(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2-methylbenzyl)piperazine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1230), except using(R)-1-(tert-butoxycarbonyl)-4-(2-methylbenzyl)piperazine-2-carboxylicacid in step 1 and 5-(aminomethyl)-6-methylpyridin-2-amine in step 3.

Example 152. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamideDihydrochloride (1349)

Step 1: Deprotection of benzyl((R)-2-((tert-butoxycarbonyl)amino)-4-phenylbutanoyl)-L-alaninate (789.3mg, 1.79 mmol) was done according to the procedure for compound 1119,step 2. The crude product was dissolved in CH₂Cl₂ and adsorbed on silicagel. Purification by chromatography (0-15% MeOH—CH₂Cl₂) afforded methyl((R)-2-amino-4-phenylbutanoyl)-L-alaninate (335.0 mg, 71% yield).

Step 2: 3-(2-Hydroxyethyl)phenol (2.1 g, 15.2 mmol) was dissolved inDMSO (8 mL) under N₂. The solution was treated dropwise with a solutionof sulfur trioxide pyridine complex (2.5 g, 15.7 mmol) in DMSO (9 mL).The reaction was stirred at room temp for 1 h, quenched with ice water,and diluted with CH₂Cl₂. The organic layer was washed with ice water (3times), washed with brine, dried (Na₂SO₄), vacuum filtered, andevaporated under vacuum. The crude product was dissolved in CH₂Cl₂ andadsorbed on silica gel. Purification by chromatography (0-100%EtOAc-hexanes) afforded the crude 2-(3-hydroxyphenyl)acetaldehyde (1.83g, 88% yield).

Step 3: Methyl ((R)-2-amino-4-phenylbutanoyl)-L-alaninate (335.0 mg,1.27 mmol) was coupled with crude 2-(3-hydroxyphenyl)acetaldehyde (417mg, 3.06 mmol) according to the procedure for compound 1130, step 2. Thecrude product was dissolved in CH₂Cl₂ and adsorbed on silica gel.Purification by chromatography (0-5% MeOH—CH₂Cl₂) afforded methyl((R)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanoyl)-L-alaninate (270mg, 61% yield).

Step 4: A mixture of((R)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanoyl)-L-alaninate (270.3mg, 0.703 mmol) in THF (3.4 mL) and water (3.4 mL) was treated with LiOH(84 mg, 3.51 mmol). The reaction was stirred for 16 h at room temp,adjusted to pH 3 with the slow addition of 10% KHSO₄ solution, extractedwith EtOAc (3 times). The organic layers were combined, washed with 5%NaHCO₃ solution, washed with brine, dried (Na₂SO₄), vacuum filtered, andevaporated under vacuum to afford the crude((R)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanoyl)-L-alanine (213.6mg, 82% yield).

Step 5: ((R)-2-((3-Hydroxyphenethyl)amino)-4-phenylbutanoyl)-L-alanine(110.6 mg, 0.299 mmol) was coupled with5-(aminomethyl)-6-methylpyridin-2-amine (66 mg, 0.481 mmol) according tothe procedure for compound 1088, step 2 except HBTU was added to thereaction at 0° C. to afford(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamide(97.6 mg, 67% yield).

Step 6:(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((3-hydroxyphenethyl)amino)-4-phenylbutanamidedihydrochloride was formed according to the procedure for compound(1319), step 6.

Example 153. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1350)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1328).

Example 154. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-4-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDihydrochloride (1351)

Step 1: 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate was synthesizedaccording to the procedures for compound (1304), step 1 to step 3.

Step 2: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate (143 mg, 0.30mmol), phenyl boronic acid (44 mg, 0.36), Pd(dppf)Cl₂ (22 mg, 0.03mmol), cesium carbonate (293 mg, 0.90 mmol), THF (3 mL) and water (0.3mL). The resulting mixture was degassed by bubbling N₂ through thesolution for 10 min. The reaction was then heated to 90° C. for 4 h.Upon cooling to room temperature, the reaction solution was filteredthrough diatomaceous earth, eluting with EtOAc, concentrated andpurified by chromatography using EtOAc-hexanes to afford 2-benzyl1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-4-ylmethyl)pyrrolidine-1,2-dicarboxylate (110mg, 78% yield) as a colorless sticky liquid.

Step 3:(2R,4S)-4-([1,1′-Biphenyl]-4-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), step 4 to step 8.

Example 155. Preparation of(R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2-((3-(trifluoromethoxy)phenethyl)amino)butanamideDi-trifluoroacetate salt (1352)

Step 1: Benzyl(imino(4-(((S)-2-((R)-4-phenyl-2-((3-(trifluoromethoxy)phenethyl)amino)butanamido)propanamido)methyl)phenyl)methyl)carbamatewas synthesized according to the procedure for compound 1130, step 2.

Step 2: Deprotection of benzyl(imino(4-(((S)-2-((R)-4-phenyl-2-((3-(trifluoromethoxy)phenethyl)amino)butanamido)propanamido)methyl)phenyl)methyl)carbamateaccording to the procedure for compound 1130, step 3. Purification byreverse phase HPLC (5-75% MeCN—H₂O) to afford(R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenyl-2-((3-(trifluoromethoxy)phenethyl)amino)butanamidedi-trifluoroacetate salt.

Example 156. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperidine-2-carboxamideDihydrochloride (1353)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1253).

Example 157. Preparation of(2S,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperidine-2-carboxamideDihydrochloride (1354)

(2S,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpiperidine-2-carboxamidewas synthesized according to the procedures for compound (1230), exceptusing 4-benzyl-1-(tert-butoxycarbonyl)piperidine-2-carboxylic acid instep 1 and 5-(aminomethyl)-6-methylpyridin-2-amine in step 3.

Example 158. Preparation of(R)-2-amino-N—((S)-1-((5-bromo-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideTrifluoroacetate salt (1355)

Steps 1-2: The title compound was synthesized as a white hygroscopicsolid according to steps 3-4 of the procedure for compound (1313) usingthe appropriate starting materials (8.3 mg, 17% yield over two steps).

Example 159. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-4-ylmethyl)-N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1356)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-4-ylmethyl)pyrrolidine-1,2-dicarboxylate wassynthesized according to the procedures for compound (1351) step 1 andstep 2.

Step 2:(2R,4S)-4-([1,1′-Biphenyl]-4-ylmethyl)-N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1307), step 1 to step 5, followed by purification byreverse-phase HPLC.

Example 160. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1357)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1351), except that the final product was purified bychromatography using reverse-phase HPLC.

Example 161. Preparation of(2R,4R)—N—((S)-1-(((2-Amino-5-chloropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1358)

Step 1: A solution of 2-amino-5-chloropyridine-3-carbonitrile (250 mg,1.62 mmol) in MeOH (5 mL) and 7 N NH₃ in MeOH (25 mL) was degassed witha stream of Ar 2 times. Raney nickel (300 mg) was added and a vacuum waspulled for 1 min. A balloon of H₂ was added and the reaction mixture wasstirred for 16 h at room temperature. Upon completion, the reactionmixture was degassed with a stream of Ar 2 times. The catalyst wasremoved by diatomaceous earth filtration and the solution was conc. Theresidue was taken up in 5% H₂O in MeOH, filtered (0.2 μm syringefilter), and the filtrate was conc under vacuum to give3-(aminomethyl)-5-chloropyridin-2-amine (189 mg, 74% yield).

Step 2: To a solution of 3-(aminomethyl)-5-chloropyridin-2-amine (47 mg,0.3 mmol) in DMF (5 mL, 0.06 mmol) was added((2R,4R)-1-(tert-butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alanine(84 mg, 0.23 mmol). The resulting mixture was cooled to 0° C. HBTU (114mg, 0.3 mmol) and DIEA (0.16 mL) were added to the above mixture. Afterstirring for 30 min at the same temperature, the reaction was warmed toroom temperature. The reaction was stirred for 90 min then conc undervacuum. The residue was dissolved in EtOAc-CH₂Cl₂ then washed with 10%KHSO₄, H₂O, sat. aq NaHCO₃, and brine. The organic layer was dried overanhyd Na₂SO₄ and conc under vacuum. The residue was purified bychromatography (0-100% [5% 7 N NH₃ in MeOH/CH₂Cl₂]—CH₂Cl₂) to givetert-butyl(2R,4R)-2-(((S)-1-(((2-amino-5-chloropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(104 mg, 90% yield).

Step 3: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((2-amino-5-chloropyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(104 mg, 0.21 mmol) was conducted according to the procedure forcompound (1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 162. Preparation of(2R,4R)-4-([1,1′-Biphenyl]-3-yl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1359)

Step 1:(R)-4-([1,1′-Biphenyl]-3-yl)-1-(tert-butoxycarbonyl)-2,5-dihydro-1H-pyrrole-2-carboxylicacid was synthesized from 1-(tert-butyl) 2-methyl(R)-4-oxopyrrolidine-1,2-dicarboxylate according to the procedures forcompound (1247), step 1 to step 3.

Step 2: Under Ar,(R)-4-([1,1′-biphenyl]-3-yl)-1-(tert-butoxycarbonyl)-2,5-dihydro-1H-pyrrole-2-carboxylicacid (347 mg, 0.95 mmol) and chlorotris(triphenylphosphine)rhodium (88mg, 0.095 mmol) were dissolved in anhydrous THF (15 mL), MeOH (15 mL),and Et₃N (0.13 mL, 0.95 mmol). The atmosphere in the flask was thenchanged to H₂ and a slight positive pressure maintained while thesolution was stirred 36 h. The volatiles were evaporated, the residuesuspended in NaHCO₃ (60 mL) and the pH adjusted to approximately 10 with1 M aq. NaOH. EtOAc (60 mL) was added and the mixture was partitioned.The organic layer was washed with another 30 mL of NaHCO₃ and thecombined aqueous layers were brought to pH 3-4 using 1 M aq. HCl; theproduct subsequently back-extracted with EtOAc (3×60 mL). The combinedorganic layers were dried over Na₂SO₄ and evaporated to furnish(2R,4R)-4-([1,1′-biphenyl]-3-yl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (175 mg, 50% yield) as an orange colored sticky liquid.

Step 3:(2R,4R)-4-([1,1′-biphenyl]-3-yl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid was coupled to(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride according to the procedure for compound (1304), step 7 togive tert-butyl(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate.

Step 4: Deprotection of tert-butyl(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylateaccording to the procedure for compound (1304), step 8, gave(2R,4R)-4-([1,1′-biphenyl]-3-yl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidewhich was purified using reverse-phase HPLC and isolated as thedi-trifluoroacetate salt.

Example 163. Preparation of(2R,4R)-4-([1,1′-Biphenyl]-3-yl)-N—((R)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1360)

tert-Butyl(2R,4R)-4-([1,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate,isolated from the preparation of tert-butyl(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(compound (1359), step 3) was deprotected according to the procedure forcompound (1304), step 8 to give(2R,4R)-4-([1,1′-biphenyl]-3-yl)-N—((R)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt after purification using reverse-phase HPLC.

Example 164. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(thiazol-2-yl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1361)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(thiazol-2-yl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), except that the final product was purified usingreverse-phase HPLC.

Example 165. Preparation of(2R,4R)—N—((S)-1-(((3-Chloro-1H-indol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(1362)

Step 1:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled with (3-chloro-1H-indol-5-yl)methanamine (synthesizedaccording to the procedures reported in WO200002611) according to theprocedure for compound (1265), step 1 to give tert-butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-indol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(71.7 mg, 62% yield).

Step 2: To a solution of tert-butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-indol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(28.7 mg, 0.055 mmol) in anhyd CH₂Cl₂ (5 mL) over an ice bath was addedTFA (6 μL), triethylsilane (2 drops). Additional TFA (6 μL) was added.After stirring for 15 min the ice bath was removed and stirringcontinued for 1 h. Additional TFA (0.25 mL) was added and the mixturewas stirred for 75 min. The reaction was quenched with slow addition of1 M NaOH (3 mL). After stirring for 5 min the mixture was cooled over anice bath. Sat. NaHCO₃ was added until the pH was neutral. The mixturewas saturated with NaCl and extracted with 10% MeOH—CH₂Cl₂. The combinedorganics were dried (Na₂SO₄) and conc in vacuo. Purification bychromatography (0-7.5% MeOH—CH₂Cl₂) gave(2R,4R)—N—((S)-1-(((3-chloro-1H-indol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(12.8 mg, 55% yield).

Example 166. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)piperidine-2-carboxamideHydrochloride (1363)

(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)piperidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1230), except using((2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)piperidine-2-carbonyl)-L-alaninein step 3.

Example 167. Preparation of(2R,4R)—N—((S)-1-((3-Chloro-5-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1364)

Steps 1-2: The title compound was synthesized as a white powderaccording to steps 3-4 of the procedure for compound 1119 using theappropriate starting materials (8.5 mg, 11% yield over two steps).

Example 168. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideHydrochloride (1365)

Steps 1-2: The title compound was synthesized as a white powderaccording to steps 1-2 of the procedure for compound (1246) using theappropriate starting materials (33 mg, 35% yield over two steps).

Example 169. Preparation of(2R,4R)—N—((S)-1-((Imidazo[1,2-a]pyridin-7-ylmethyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1366)

(2R,4R)—N—((S)-1-((Imidazo[1,2-a]pyridin-7-ylmethyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedure given forcompound (1323), steps 2 and 3.

Example 170. Preparation of(S)—N-(1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-3-benzyl-1H-pyrazole-5-carboxamide(1367)

(S)—N-(1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-3-benzyl-1H-pyrazole-5-carboxamidewas synthesized according to the procedures for compound (1230), exceptusing 3-benzyl-1H-pyrazole-5-carboxylic acid in step 1 and5-(aminomethyl)-6-methylpyridin-2-amine in step 3.

Example 171. Preparation of(R)-2-((4-Acetamidophenethyl)amino)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamideDihydrochloride (1368)

Step 1: Benzyl ((R)-2-amino-4-phenylbutanoyl)-L-alaninate (403.0 mg,1.18 mmol) was coupled with N-(4-(2-oxoethyl)phenyl)acetamide (251.0 mg,1.42 mmol) according to the procedure for compound 1130, step 2. Thecrude product was dissolved in CH₂Cl₂ and adsorbed on silica gel.Purification by chromatography (0-10% MeOH—CH₂Cl₂) afforded benzyl((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alaninate(500.1 mg, 84% yield).

Step 2: Deprotection of benzyl((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alaninate(500.1 mg, 0.997 mmol)) according to the procedure for compound 1119,step 2 afforded methyl((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alaninate(122.0 mg, 29% yield).

Step 3: Hydrolysis of methyl((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alaninate(122.0 mg, 0.287 mmol) according to the procedure for compound (1349),step 4 afforded the crude((R)-2-((4-acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alanine (37.5mg, 32% yield).

Step 4: ((R)-2-((4-Acetamidophenethyl)amino)-4-phenylbutanoyl)-L-alanine(37.5 mg, 0.091 mmol) was coupled with5-(aminomethyl)-6-methylpyridin-2-amine (21.0 mg, 0.15 mmol) accordingto the procedure for compound 1088, step 2 except HBTU was added to thereaction at 0° C. The crude product was dissolved in CH₂Cl₂ and adsorbedon silica gel. Purification by chromatography (0-15% MeOH—CH₂Cl₂)afforded(R)-2-((4-acetamidophenethyl)amino)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(31.1 mg, 64% yield).

Step 5:(R)-2-((4-Acetamidophenethyl)amino)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamidedihydrochloride was formed according to the procedure for compound(1319), step 6.

Example 172. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-(3-methylbenzyl)pyrrolidine-2-carboxamideHydrochloride (1369)

Steps 1-2: A 250 mL round bottom flask was charged withN-(tert-butoxycarbonyl)-L-alanine (503 mg, 2.66 mmol) and ACN (13 mL)then cooled to 0° C. Oxyma (435 mg, 3.06 mmol) and EDC (560 mg, 2.92mmol) were added portion-wise and allowed to stir for 10 min.2-(Aminomethyl)-4-chloro-6-methylphenol (500 mg, 2.92 mmol) and DIEA(695 μL, 4 10 mmol) were then added, respectively, and the reactionallowed to slowly warm to ambient temperature overnight. The solvent wasremoved under reduced pressure and the residue re-dissolved in EtOAcbefore being washed with 10% aq. KHSO₄ and brine, dried over Na₂SO₄ andconcentrated in vacuo. The crude product was purified by chromatography(60-70% EtOAc/hexanes). tert-Butyl(S)-(1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamatewas dissolved in conc. HCl in MeOH (10 mL) and stirred at ambienttemperature overnight. The reaction mixture was then concentrated andpurified by chromatography (MeOH/CH₂Cl₂ containing 2.5% 7 N NH₃-MeOH) toyield (S)-2-amino-N-(5-chloro-2-hydroxy-3-methylbenzyl)propenamide as ayellow powder (469 mg, 73% yield over two steps).

Steps 3-4: The title compound was synthesized as a white solid accordingto steps 1-2 of the procedure for compound (1246) using the appropriatestarting materials (11 mg, 15% yield over two steps).

Example 173. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamide(1370)

Steps 1-2: The title compound was synthesized as a white solid accordingto steps 3-4 of the procedure for compound (1313) using the appropriatestarting materials (17.4 mg, 36% yield over two steps).

Example 174. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1371)

(2R,4S)-4-Benzyl-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1307).

Example 175. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2-bromobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1372)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2-bromobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328), except that the final product was purified usingreverse-phase HPLC.

Example 176. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-2-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1373)

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (2.0 g, 6.28 mmol) in THF (40 mL)at −78° C. was slowly added lithium bis(trimethylsilyl)amide (6.90 mL,6.90 mmol, 1 M in THF) under Ar. After stirring for 1 h at −78° C.,2-bromobenzyl bromide (1.88 g, 7.53 mmol) was added and the stirringcontinued for an additional 2 h. The reaction mixture was quenched withsat. NH₄Cl solution and extracted with diethyl ether (3×60 mL). Thecombined extracts were dried over Na₂SO₄, filtered and concentratedunder vacuum. The residue was purified by chromatography (EtOAc-hexanes)gave 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (2.63 g,86% yield).

Step 2: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (1.60 g,3.91 mmol) in THF (22 mL) at −78° C. was added lithiumtriethylborohydride solution (3.94 mL, 3.94 mmol, 1 M in THF) under Aratmosphere. After 30 min, the reaction mixture was quenched with sat.NaHCO₃ solution (8.60 mL) and warmed to 0° C. At 0° C., 30% H₂O₂(about25 drops) was added and the reaction mixture was stirred at sametemperature for 30 min. The organic volatiles were removed under vacuumand the aqueous layer was extracted with CH₂Cl₂ (3×40 mL). The combinedorganic extracts were thoroughly dried using Na₂SO₄, filtered,concentrated to afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate (1.60 gcrude) that was directly used in the next step without furtherpurification.

Step 3: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate (1.60 gcrude) and triethylsilane (0.63 mL, 3.94 mmol) in CH₂Cl₂ at −78° C. wasdropwise added boron trifluoride diethyl etherate (0.49 mL, 3.94 mmol)under Ar atmosphere. After 30 min at same temperature additionaltriethylsilane (0.63 mL, 3.94 mmol) and boron trifluoride diethyletherate (0.49 mL, 3.94 mmol) were added. After stirring for 2 h at −78°C., the reaction mixture was quenched with sat. aqueous NaHCO₃ solution(10 mL) and extracted with CH₂Cl₂(3×40 mL). The combined extracts weredried over Na₂SO₄, filtered and conc under vacuum. The residue waspurified by chromatography (EtOAc-hexanes) to afford 2-benzyl1-(tert-butyl) (2R,4S)-4-(2-bromobenzyl)pyrrolidine-1,2-dicarboxylate(931 mg, 60% yield in two steps).

Step 4: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)pyrrolidine-1,2-dicarboxylate (200 mg, 0.42mmol), phenyl boronic acid (62 mg, 0.51), Pd(dppf)Cl₂ (31 mg, 0.042mmol), cesium carbonate (413 mg, 1.26 mmol), THF (4.2 mL) and water(0.42 mL). The resulting mixture was degassed by bubbling N₂ through thesolution for 10 min. The reaction was then heated to 90° C. for 4 h.Upon cooling to room temperature, the reaction solution was filteredthrough diatomaceous earth, eluted with EtOAc, concentrated and purifiedby chromatography using EtOAc-hexanes to afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)pyrrolidine-1,2-dicarboxylate (200mg, 99% yield) as a colorless sticky liquid.

Step 4: A solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)pyrrolidine-1,2-dicarboxylate (200mg, 0.42 mmol) in MeOH (4.2 mL) was bubbled with Ar gas for 5 minutes.10% Pd/C (20 mg) was added to the reaction mixture and that was stirredunder 1 atm of H₂ for 3 h. The reaction mixture was filtered (0.2 μmsyringe filter) and the filtrate was concentrated under vacuum to give(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (150 mg, 93% yield).

Step 5: To a stirred solution of (tert-butoxycarbonyl)-L-alanine (1.96g, 10.38 mmol) in CH₂Cl₂ (55 mL) was added NHS (1.25 g, 10.89 mmol) atroom temperature. To the reaction mixture DCC (2.25 g 10.9 mmol) wasadded and the reaction mixture stirred for 1.0 h.5-(Aminomethyl)-6-methylpyridin-2-amine was added to the reactionmixture and sonicated for 5 min. The5-(aminomethyl)-6-methylpyridin-2-amine was completely dissolved and thereaction mixture was stirred at ambient temperature for 1 h. The crudereaction mixture was filtered and conc under reduced pressure. Purifiedthe crude reaction mixture by chromatography using MeOH—CH₂Cl₂ to affordtert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 70% yield) as a white solid.

Step 6: To tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 7.62 mmol) was added a solution of MeOH—HCl (19 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (typically 1 h). The solution was evaporated todryness and MeOH (50 mL) was added and evaporated to dryness to removeresidual HCl gas to give(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (1.60 g, 90% yield) as an off white solid (hygroscopic).

Step 7: To a stirred solution of(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (38 mg, 0.1 mmol) in anhydrous DMF (1 mL) was added HOBt (24 mg,0.11 mmol), DIEA (0.1 mL, 0.52 mmol) and EDC (28 mg, 0.11 mmol) atambient temperature. The reaction mixture was stirred for 30 min atambient temperature.(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (23 mg, 0.12 mmol) was added to the reaction mixture andstirred overnight. The solution was evaporated to dryness and theresidue was partitioned with EtOAc (10 mL) and 10% KHSO₄ (5 mL). Theorganic layer was separated and washed with sat. NaHCO₃ solution (10ml), dried over anhydrous Na₂SO₄ and cone under vacuum. The crudereaction mixture was purified by chromatography using MeOH—CH₂Cl₂ toafford tert-butyl(2R,4S)-4-([11,1′-biphenyl]-2-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(40 mg, 70% yield) as a white solid.

Step 8: To tert-butyl(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(40 mg, 0.07 mmol) in 1 mL CH₂Cl₂ was added TFA (0.11 mL, 1.39 mmol)with stirring at ambient temperature while monitoring for theconsumption of starting material (30 min to 1h). The solution wasevaporated to dryness and MeOH (10 mL) was added and evaporated todryness to remove residual TFA. The resulting crude reaction mixture waspurified using reverse-phase HPLC to afford(2R,4S)-4-([1,1′-biphenyl]-2-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt (22.2 mg, 67% yield) as a white solid.

Example 177. Preparation of(2R,4S)-4-(4-bromobenzyl)-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1374)

Steps 1-2: tert-Butyl(2R,4S)-4-(4-bromobenzyl)-2-(((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylatewas synthesized according to step 3 of the procedure for compound 1119using the appropriate starting materials. Removal of the Boc group wasachieved using the procedure from step 4 for compound (1313). The crudeproduct was purified by chromatography (MeOH/CH₂Cl₂ containing 2.5% 7 NNH₃-MeOH), then the collected fractions were concentrated, treated with1 N HCl and lyophilized to yield the title compound as a white powder(28 mg, 47% yield over 2 steps).

Example 178. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((4-chlorobenzyl)amino)-4-phenylbutanamide(1375)

(R)-2-Amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(148.5 mg, 0.246 mmol) was coupled with 4-chlorobenzaldehyde (45 mg,0.320 mmol) according to the procedure for compound 1130, step 2. Thecrude product was dissolved in CH₂Cl₂ and adsorbed on silica gel.Purification by chromatography (0-5% MeOH—CH₂Cl₂) afforded(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((4-chlorobenzyl)amino)-4-phenylbutanamide(57.3 mg, 44% yield).

Example 179. Preparation of(S)—N′-((6-Amino-2-methylpyridin-3-yl)methyl)-2-((R)-2-amino-4-phenylbutanamido)pentanediamideDi-trifluoroacetate (1376)

Step 1: tert-Butyl((R)-1-(((S)-5-amino-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1,5-dioxopentan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(49 mg, 17% yield) was synthesized from((R)-2-amino-4-phenylbutanoyl)-L-glutamine (230 mg, 0.56 mmol, preparedaccording to the procedure for compound (1335), step 1-2 and5-(aminomethyl)-6-methylpyridine-2-amine according to the procedure forcompound (1326), step 3.

Step 2: Deprotection of tert-butyl((R)-1-(((S)-5-amino-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1,5-dioxopentan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamate(49 mg, 0.09 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 180. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-(pentylamino)-4-phenylbutanamideDi-trifluoroacetate salt (1377)

Step 1:(R)-2-Amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(99.0 mg, 0.224 mmol) was coupled with pentanal (30 μL, 0.282 mmol)according to the procedure for compound 1130, step 2. The crude productwas dissolved in CH₂Cl₂ and adsorbed on silica gel. Purification bychromatography (0-5% MeOH—CH₂Cl₂) afforded(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-(pentylamino)-4-phenylbutanamide(12.5 mg, 13% yield).

Step 2: To a solution of(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-(pentylamino)-4-phenylbutanamidein CH₂Cl₂ (1 mL) was added TFA (0.5 mL). Volatile was evaporated undervacuum to afford of(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-(pentylamino)-4-phenylbutanamidedi-trifluoroacetate salt.

Example 181. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyclobutylbenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1378)

(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyclobutylbenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1356).

Example 182. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyclobutylbenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1379)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate was synthesizedaccording to the procedures for compound (1304), step 1 to step 3.

Step 2: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate (200 mg, 0.42mmol), cyclobutyl boronic acid (84 mg, 0.84), Pd(dppf)Cl₂ (31 mg, 0.042mmol), K₃PO₄ (180 mg, 0.84 mmol), Toluene (3 mL) and water (0.3 mL). Theresulting mixture was degassed by bubbling N₂ through the solution for10 min. The reaction was then heated to 90° C. for 16 h. Upon cooling toroom temperature, the reaction solution was filtered throughdiatomaceous earth, eluting with EtOAc, concentrated and purified bychromatography using EtOAc/hexanes to afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-cyclobutylbenzyl)pyrrolidine-1,2-dicarboxylate (30 mg, 16%yield) as a colorless sticky liquid.

Step 3:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyclobutylbenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), step 4 to step 8, except that the final product waspurified using reverse-phase HPLC.

Example 183. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(tert-butyl)benzyl)pyrrolidine-2-carboxamideDihydrochloride (1380)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(tert-butyl)benzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 184. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((4-(morpholine-4-carbonyl)benzyl)amino)-4-phenylbutanamideDi-trifluoroacetate salt (1381)

Step 1:(R)-2-Amino-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylbutanamide(42.5 mg, 0.115 mmol) was coupled with4-(morpholine-4-carbonyl)benzaldehyde (37.5 mg, 0.171 mmol) according tothe procedure for compound 1130, step 2. The crude product was dissolvedin CH₂Cl₂ and adsorbed on silica gel. Purification by chromatography(0-10% MeOH—CH₂Cl₂) afforded(R)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((4-(morpholine-4-carbonyl)benzyl)amino)-4-phenylbutanamide(21.4 mg, 32% yield).

Step 2:(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2-((4-(morpholine-4-carbonyl)benzyl)amino)-4-phenylbutanamidedi-trifluoroacetate salt was formed according to the procedure forcompound (1368), step 2.

Example 185. Preparation of(S)—N′-((6-Amino-2-methylpyridin-3-yl)methyl)-2-((2R,4S)-4-benzylpyrrolidine-2-carboxamido)pentanediamideDi-trifluoroacetate salt (1382)

Step 1: Methyl ((2R,4S)-4-benzylpyrrolidine-2-carbonyl)-L-glutaminate(130 mg, 84% yield) was synthesized from(2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid(106 mg, 0.35 mmol) and L-glutamine methyl ester hydrochloride accordingto the procedure for compound (1326), step 1.

Step 2: ((2R,4S)-4-Benzylpyrrolidine-2-carbonyl)-L-glutamine (123 mg,96% yield) was synthesized from methyl((2R,4S)-4-benzylpyrrolidine-2-carbonyl)-L-glutaminate (130 mg, 0.29mmol) according to the procedure for compound (1326), step 2 except thatthe crude material was applied to the next step without furtherpurification.

Step 3: tert-Butyl(2R,4S)-2-(((S)-5-amino-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1,5-dioxopentan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(125 mg, 81% yield) was synthesized from((2R,4S)-4-benzylpyrrolidine-2-carbonyl)-L-glutamine (123 mg, 0.28 mmol)and 5-(aminomethyl)-6-methylpyridine-2-amine according to the procedurefor compound (1326), step 3.

Step 4: Deprotection of tert-butyl(2R,4S)-2-(((S)-5-amino-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1,5-dioxopentan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(125 mg, 0.23 mmol) was conducted according to the procedure forcompound (1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 186. Preparation of(2R,4R)—N—((S)-1-((2-Hydroxy-3,5-dimethylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideHydrochloride (1383)

Steps 1-2: tert-Butyl(2R,4S)-4-(4-bromobenzyl)-2-(((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylatewas synthesized according to step 3 of the procedure for compound 1119using the appropriate starting materials. Removal of the Boc group wasachieved using the procedure from step 4 for compound (1313) to yieldthe title compound as a beige solid (17.4 mg, 39% over two steps).

Example 187. Preparation of(2R,4R)—N—((S)-1-(((3-Chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1384)

Step 1: To a solution of 1H-pyrazolo[3,4-b]pyridine-5-carbonitrile (303mg, 2.1 mmol) in anhyd DMF (5 mL) under Ar was added NCS (280 mg, 2.1mmol). The mixture was heated at 40° C. for 18 h after which the heatwas increased to 55° C. After heating for 5 h, additional NCS (134 mg,1.0 mmol) was added and heating continued for 30 min. The mixture wasslowly cooled to ambient temperature then H₂O was added. The mixture wasextracted with EtOAc and the combined organics were washed with H₂O,sat. NaHCO₃ and brine then dried (Na₂SO₄) and conc in vacuo. The solidwas chromatographed (0-40% EtOAc-hexanes) to give3-chloro-1H-pyrazolo[3,4-b]pyridine-5-carbonitrile (216 mg, 58% yield).

Step 2: 3-Chloro-1H-pyrazolo[3,4-b]pyridine-5-carbonitrile was reducedaccording to the procedure given for compound (1323), step 1. Followingfiltration of the reaction mixture through diatomaceous earth and concin vacuo, the solid was dissolved in 1 M HCl and washed with EtOAc 3×.The aq layer was conc in vacuo to give(3-chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methanamine as a tan solid (184mg, 60% yield).

Step 3:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to (3-chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methanamineaccording to the procedure given for (1280). Purification bychromatography (0-5% MeOH—CH₂Cl₂) gave the product contaminated withacid starting material. The product was dissolved in EtOAc, washed withsat. NaHCO₃ 3×, brine then dried over Na₂SO₄ and conc in vacuo to givetert-butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(81 mg, 61% yield).

Step 4: tert-Butyl(2R,4R)-2-(((S)-1-(((3-chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure given for compound (1311),step 3 to give(2R,4R)—N—((S)-1-(((3-chloro-1H-pyrazolo[3,4-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (67.6 mg, 88% yield).

Example 188. Preparation of(2R,4S)—N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamideTrifluoroacetate salt (1385)

Steps 1-2: tert-Butyl(S)-(1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamatewas synthesized according to steps 3-4 of the procedure for compound(1313) using the appropriate starting materials (3.54 g, 76% yield overtwo steps).

Steps 3-4: The title compound was synthesized as a white powderaccording to steps 3-4 of the procedure for compound (1313) using theappropriate starting materials (15 mg, 40% yield over two steps).

Example 189. Preparation of(2R,4R)—N—((S)-1-((3-Chloro-5-cyanobenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1386)

Step 1: tert-Butyl((R)-1-(((S)-1-((3-chloro-5-cyanobenzyl)amino)-1-oxopropan-2-yl)amino)-1-oxo-4-phenylbutan-2-yl)carbamatewas synthesized as a colorless oil (95 mg, 62% yield) according to step1 of the procedure for compound (1246) using the appropriate startingmaterials.

Step 2: Removal of the Boc group was achieved using procedure from step4 for compound (1313) to yield the title compound as a white powder (21mg, 67% yield).

Example 190. Preparation of(2R,4R)—N—((S)-1-((3-Carbamoyl-5-chlorobenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1387)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-((3-chloro-5-cyanobenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(65 mg, 0.13 mmol) was dissolved in EtOH (0.5 mL) and added dropwise toa stirring mixture of urea hydrogen peroxide (72 mg, 0.76 mmol) and NaOH(18 mg, 0.46 mmol) in H₂O (1.2 mL) at 0° C., then allowed to warm toambient temperature over 2 h. Upon completion, the reaction mixture wasdiluted in EtOAc, washed with 10% aq. KHSO₄ and brine. The organic layerwas dried over Na₂SO₄, concentrated and purified by chromatography. Theintermediate was then dissolved in CH₂Cl₂ (2 mL) and treated with TFA(0.5 mL) at ambient temperature for 2 h, before being concentrated tofurnish the title compound as a white powder (28 mg, 40% yield over twosteps).

Example 191. Preparation ofN—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-7,7-dimethyl-5-oxo-4-phenyl-1,4,5,6,7,8-hexahydroquinoline-2-carboxamide(1388)

N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-7,7-dimethyl-5-oxo-4-phenyl-1,4,5,6,7,8-hexahydroquinoline-2-carboxamidewas synthesized according to the procedure for compound (1304), step 7using7,7-dimethyl-5-oxo-4-phenyl-1,4,5,6,7,8-hexahydroquinoline-2-carboxylicacid.

Example 192. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamideHydrochloride (1389)

(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamidehydrochloride was synthesized according to the procedures for compound(1304), steps 7 and 8 using(3R)-2-(tert-butoxycarbonyl)-2,3,4,4a,9,9a-hexahydro-1H-pyrido[3,4-b]indole-3-carboxylicacid.

Example 193. Preparation of(2R,4R)—N—((S)-1-(((3-Aminobenzo[d]isoxazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1390)

Step 1: To a solution of 4-aminomethyl-2-fluoro-benzonitrilehydrochloride (1.0 g, 5.35 mmol) in MeOH (10 mL) and MeCN (10 mL) wasadded Et₃N (2.2 mL, 16.05 mmol), di-tert-butyl dicarbonate (1.4 g, 6.43mmol) and DMAP (653 mg, 5.35 mmol). After stirring for 16 h, thereaction mixture was conc and the residue was partitioned with EtOAc andH₂O. The organic layer was separated, washed with brine, dried overanhyd Na₂SO₄, and conc under vacuum. The residue was purified bychromatography (0-100% EtOAc-hexanes) to give tert-butyl(4-cyano-3-fluorobenzyl)carbamate (1.13 g, 88% yield).

Step 2: To a solution of acetohydroxamic acid in anhyd DMF was addedKO^(t)Bu (1 M in THF, 7.1 mL, 7.1 mmol). After stirring for 30 min atambient temperature, tert-butyl (4-cyano-3-fluorobenzyl)carbamate (1.13g, 4.73 mmol) was added to the above mixture. After stirring for 19 h atthe same temperature, the reaction was quenched by addition of H₂O andextracted with EtOAc. The organic layer was washed with brine, driedover anhyd Na₂SO₄, and conc under vacuum. The residue was purified bychromatography (0-100% EtOAc-hexanes) to give tert-butyl((3-aminobenzo[d]isoxazol-6-yl)methyl)carbamate (925 mg, 74% yield).

Step 3: Deprotection of tert-butyl((3-aminobenzo[d]isoxazol-6-yl)methyl)carbamate (125 mg, 0.48 mmol) wasconducted according to the procedure for compound (1259), step 2 to give6-(aminomethyl)benzo[d]isoxazol-3-amine di-trifluoroacetate salt (186mg, 100% yield).

Step 4: tert-Butyl(2R,4R)-2-(((S)-1-(((3-aminobenzo[d]isoxazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(153 mg, 84% yield) was synthesized from6-(aminomethyl)benzo[d]isoxazol-3-amine di-trifluoroacetate salt (130mg, 0.47 mmol) according to the procedure for compound (1358), step 2.

Step 5: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((3-aminobenzo[d]isoxazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(153 mg, 0.3 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 194. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(2-oxopyrrolidin-1-yl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1391)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate was synthesizedaccording to the procedures for compound (1304), step 1 to step 3.

Step 2: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromobenzyl)pyrrolidine-1,2-dicarboxylate (120 mg, 0.25mmol), 2-pyridone (43 mg, 0.51), BrettPhos palladacycle (4.2 mg, 0.005mmol), K₃PO₄ (108 mg, 0.51 mmol), tert-butanol (1.2 mL). The resultingmixture was degassed by bubbling N₂ through the solution for 5 min. Thereaction was then heated to 100° C. for 12 h. Upon cooling to roomtemperature, the reaction solution was filtered through diatomaceousearth, eluting with EtOAc, concentrated and purified by chromatographyusing EtOAc-hexanes to afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-(2-oxopyrrolidin-1-yl)benzyl)pyrrolidine-1,2-dicarboxylate(30 mg, 25% yield) as a colorless oil.

Step 3:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-(2-oxopyrrolidin-1-yl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), step 4 to step 8, except that the final product waspurified using reverse-phase HPLC.

Example 195. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamideDi-Trifluoroacetate salt (1392)

(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-2-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1334).

Example 196. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-2-ylmethyl)-N—((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1393)

(2R,4S)-4-([1,1′-Biphenyl]-2-ylmethyl)-N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1356).

Example 197. Preparation of(2R,4R)—N—((S)-1-((5-chloro-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate (1394)

Step 1: 2-Amino-5-chlorobenzonitrile (1g, 6.55 mmol) was dissolved inEtOH (5 mL) and H₂O (10 mL), then treated with tetrafluoroboric acid(48% in H₂O; 1.7 mL, 13.1 mmol) and cooled to 0° C. Sodium nitrite (497mg, 7.2 mmol) in H₂O (10 mL) was added dropwise to the stirring mixture.After 1 h, the suspension was filtered using cold Et₂O and H₂O thendried under vacuum to yield the diazonium tetrafluoroborate salt as ayellow solid (502 mg, 31% yield).

Step 2: The diazonium salt (502 mg, 2 mmol) and CF₃CO₂Ag (530 mg, 2.4mmol) were suspended in dry THF (20 mL) and cooled to −78° C. under Ar.Et₃N (418 μL, 3 mmol) was added dropwise followed by TMSCHN₂ (2 M inhexanes; 1.1 mL, 2.2 mmol) after 10 minutes. The reaction mixture wasallowed to stir for 1 h before slowly warming to ambient temperature andquenched with CsF (304 mg, 2 mmol) in MeOH. After 30 minutes, EtOAc andbrine were added, then the organic layer separated and dried over Na₂SO₄and concentrated. Purification by chromatography (30-40% EtOAc/hexanes)furnished 5-chloro-2-(2H-tetrazol-2-yl)benzonitrile as a brown solid (86mg, 21% yield).

Step 3: A solution of 5-chloro-2-(2H-tetrazol-2-yl)benzonitrile (86 mg,0.42 mmol) in 7 N NH₃ in MeOH (5 mL) was degassed with an Ar balloon.Raney nickel (˜40 mg) was added and a vacuum was pulled for 0.5 minprior to backfilling with a balloon of H₂. The reaction mixture wasstirred for 16 h at ambient temperature. Upon completion, the catalystwas removed by filtration through diatomaceous earth and the solutionconcentrated in vacuo to give(5-chloro-2-(2H-tetrazol-2-yl)phenyl)methanamine (78 mg, 89% yield) as abrown oil.

Steps 4-5: The title compound was synthesized as a white powderaccording to steps 3-4 of the procedure for compound (1313) using theappropriate starting materials, except with purification by prep HPLC(2.3 mg, 3% yield over two steps).

Example 198. Preparation of(2R,4R)—N—((S)-1-((3,5-dichloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate (1395)

Steps 1-2: tert-Butyl(2R,4R)-2-(((S)-1-((3,5-dichloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatesynthesized according to step 1 of the procedure for compound (1242)using the appropriate starting materials. Removal of the Boc group wasachieved according to step 4 of compound (1313) to yield the titlecompound as a white crystalline solid (23 mg, 35% yield over two steps).

Example 199. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-cyano-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamide(1396)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-cyano-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamidewas synthesized according to the procedures for compound (1351), exceptthat the free base was isolated after purification by columnchromatography (0-10% [7 N NH₃-MeOH]—CH₂Cl₂).

Example 200. Preparation of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-carbamoyl-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1397)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-carbamoyl-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1351), except that the final product was purified usingreverse-phase HPLC.

Example 201. Preparation of2-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)aceticacid Trifluoroacetate salt (1398)

To a stirred solution of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidedihydrochloride (1253) (10 mg, 0.021 mmol) in CH₂Cl₂ (1 mL) and NEt₃(0.3 mL) was added benzyl 2-bromoacetate (48 mg, 0.21 mmol) under Aratmosphere. After stirring for 24 h at ambient temperature the reactionmixture was concentrated and dissolved in MeOH. To the solution wasadded 10% Pd/C (50 mg) and stirred under H₂ atmosphere at roomtemperature for 18 h. The reaction mixture was filtered overdiatomaceous earth and washed with MeOH. The organic washes wereconcentrated and purified by reverse-phase HPLC to yield2-((2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)aceticacid trifluoroacetate salt (6.2 mg, 52% yield over 2 steps).

Example 202. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1399)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4R)-4-((4-bromothiophen-2-yl)methyl)-5-oxopyrrolidine-1,2-dicarboxylatewas synthesized according to the procedure for compound (1304).

Step 2: A solution of 2-benzyl 1-(tert-butyl)(2R,4R)-4-((4-bromothiophen-2-yl)methyl)-5-oxopyrrolidine-1,2-dicarboxylate(270 mg, 0.55 mmol) and phenylboronic acid (0.66 mmol, 1.2 equiv.) inTHF/2M K₂CO₃ (1:1) was degassed with a stream of Ar for 5 min. Pd(PPh₃)₄(0.05 equiv.) was added and the solution was heated at 60° C. overnight.THF was removed by evaporation and the solution was extracted withEtOAc. The organic layer was dried over Na₂SO₄ and evaporated. Columnchromatography (10% EtOAc-hexanes) gave 2-benzyl 1-(tert-butyl)(2R,4R)-5-oxo-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-1,2-dicarboxylate(141 mg, 53% yield) as an oil.

Step 3: 2-Benzyl 1-(tert-butyl)(2R,4R)-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-1,2-dicarboxylatewas synthesized according to the procedure for compound (1304).

Step 4: To a solution of 2-benzyl 1-(tert-butyl)(2R,4R)-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-1,2-dicarboxylate(100 mg, 0.21 mmol) in THF (2.0 ml) and MeOH (1.0 ml) was added LiOH(3.14 mmol, 15.0 equiv.) in H₂O (1.0 ml) with stirring at room temp.overnight. The solution was evaporated to dryness and H₂O (5.0 ml) wasadded to the residue with swirling. The aqueous layer was extracted withether, separated, pH adjusted to 5 with 10% KHSO₄ and extracted withCH₂Cl₂. The organic layer was dried over Na₂SO₄ and evaporated giving(2R,4R)-1-(tert-butoxycarbonyl)-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-2-carboxylicacid (75 mg, 93% yield) as a foamy white solid.

Steps 5-6:(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-phenylthiophen-2-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 203. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1,2,3,4-tetrahydrobenzo[4,5]thieno[2,3-c]pyridine-3-carboxamideHydrochloride (1400)

(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1,2,3,4-tetrahydrobenzo[4,5]thieno[2,3-c]pyridine-3-carboxamidehydrochloride was synthesized according to the procedures for compound(1304), steps 7 and 8 using(R)-2-(tert-butoxycarbonyl)-1,2,3,4-tetrahydrobenzo[4,5]thieno[2,3-c]pyridine-3-carboxylicacid.

Example 204. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-2-ylmethyl)-N—((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1401)

Step 1-2: The title compound was synthesized as a white powder (7.4 mg,27% yield) according to steps 3-4 of the procedure for compound (1313)using the appropriate starting materials, except with purification ofthe crude product by chromatography (MeOH/CH₂Cl₂ containing 2.5% 7 NNH₃-MeOH), followed by treatment with 1 N HCl and lyophilizationovernight.

Example 205. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-2-ylmethyl)-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideTrifluoroacetate (1402)

Steps 1-2: The title compound was synthesized as a white solid accordingto steps 3-4 of the procedure for compound (1313) using the appropriatestarting materials (11 mg, 33% yield over two steps).

Example 206. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-(aminomethyl)-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamide(1403)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2′-(aminomethyl)-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)pyrrolidine-2-carboxamidewas synthesized from (1396) according the procedure given for compound(1304), step 4.

Example 207. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-2-carboxamideHydrochloride (1404)

Step 1: tert-Butyl(2R,4S)-2-(((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-1-carboxylate(47 mg, 80% yield) was synthesized from(S)-2-amino-N-(5-chloro-2-(1H-tetrazol-1-yl)benzyl)propanamidetrifluoroacetate (28 mg, 0.10 mmol) according to the procedure forcompound (1304), step 7.

Step 2:(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-2-carboxamidehydrochloride (43 mg, 90% yield) was synthesized from tert-butyl(2R,4S)-2-(((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(4-(pyridin-3-yl)benzyl)pyrrolidine-1-carboxylate(47 mg, 0.07 mmol) according to the procedure for compound (1304), step8.

Example 208. Preparation of(2R,4S)-4-((2′-Carbamoyl-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1405)

(2R,4S)-4-((2′-Carbamoyl-4′-fluoro-[1,1′-biphenyl]-4-yl)methyl)-N—((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1404).

Example 209. Preparation of(2R,4S)-4-([1,1′-Biphenyl]-3-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDihydrochloric acid (1406)

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (3.25 g, 10.2 mmol) in THF (60mL) at −78° C. was slowly added lithium bis(trimethylsilyl)amide (11.25mL, 11.25 mmol, 1 M in THF) under Ar atmosphere. After stirring for 1 hat −78° C., 3-bromobenzyl bromide (2.80 g, 11.25 mmol) was added and thestirring continued for an additional 2 h. The reaction mixture wasquenched with sat. NH₄Cl solution and extracted with diethyl ether(3×100 mL). The combined extracts were dried over Na₂SO₄, filtered andconcentrated under vacuum. The residue was purified by chromatography(EtOAc-hexanes) gave 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (3.47 g,70% yield).

Step 2: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (3.47 g,7.12 mmol) in THF (47 mL) at −78° C. was added lithiumtriethylborohydride solution (7.83 mL, 7.83 mmol, 1 M in THF) under Aratm. After 30 min, the reaction mixture was quenched with sat. NaHCO₃solution (20 mL) and warmed to 0° C. At 0° C., 30% H₂O₂(about 60 drops)was added and the reaction mixture was stirred at same temperature for30 min. The volatiles were removed under vacuum and the aqueous layerwas extracted with CH₂Cl₂ (3×60 mL). The combined organic extracts werethoroughly dried using Na₂SO₄, filtered, concentrated to afford 2-benzyl1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate (3.30 gcrude) that was directly used in the next step without furtherpurification.

Step 3: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate (3.30 gcrude) and triethylsilane (1.25 mL, 7.80 mmol) in CH₂Cl₂ (36 mL) at −78°C. was drop wise added boron trifluoride diethyl etherate (0.95 mL, 7.80mmol) under Ar atm. After 30 min at same temperature additionaltriethylsilane (1.25 mL, 7.80 mmol) and boron trifluoride diethyletherate (0.95 mL, 7.80 mmol) were added. After stirring for 2 h at −78°C., the reaction mixture was quenched with sat. aqueous NaHCO₃ solution(20 mL) and extracted with CH₂Cl₂ (3×60 mL). The combined extracts weredried over Na₂SO₄, filtered and conc under vacuum. The residue waspurified by chromatography (EtOAc-hexanes) to afford 2-benzyl1-(tert-butyl) (2R,4S)-4-(3-bromobenzyl)pyrrolidine-1,2-dicarboxylate(1.60 g, 47% yield in two steps).

Step 4: In a 50 mL round bottom flask equipped with a stir bar andseptum was added 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)pyrrolidine-1,2-dicarboxylate (200 mg, 0.42mmol), phenyl boronic acid (62 mg, 0.51), Pd(dppf)Cl₂ (31 mg, 0.042mmol), cesium carbonate (413 mg, 1.26 mmol), THF (4.2 mL) and water(0.42 mL). The resulting mixture was degassed by bubbling N₂ through thesolution for 10 min. The reaction was then heated to 90° C. for 4 h.Upon cooling to ambient temperature, the reaction solution was filteredthrough diatomaceous earth, eluting with EtOAc, concentrated andpurified by chromatography using EtOAc-hexanes to afford 2-benzyl1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)pyrrolidine-1,2-dicarboxylate (167mg, 83% yield) as a colorless sticky liquid.

Step 4: A solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)pyrrolidine-1,2-dicarboxylate (167mg, 0.35 mmol) in MeOH (3 mL) was bubbled with Ar gas for 5 minutes. 10%Pd/C (17 mg) was added to the reaction mixture and that was stirredunder 1 atm of H₂ for 3 h. The reaction mixture was filtered (0.2 μmsyringe filter) and the filtrate was concentrated under vacuum to give(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (130 mg, 96% yield).

Step 5: To a stirred solution of (tert-butoxycarbonyl)-L-alanine (1.96g, 10.38 mmol) in CH₂Cl₂ (55 mL) was added NHS (1.25 g, 10.89 mmol) atroom temperature. To the reaction mixture DCC (2.25 g 10.9 mmol) wasadded and the reaction mixture stirred for 1.0 h.5-(Aminomethyl)-6-methylpyridin-2-amine was added to the reactionmixture and sonicated for 5 min. The5-(aminomethyl)-6-methylpyridin-2-amine was completely dissolved andstirred the reaction mixture at ambient temperature for 1 h. The crudereaction mixture was filtered and conc under reduced pressure. The crudereaction mixture was purified by chromatography using MeOH—CH₂Cl₂ toafford tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 70% yield) as a white solid.

Step 6: To tert-butyl(S)-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(2.35 g, 7.62 mmol) was added a solution of MeOH—HCl (19 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (typically 1 h). The solution was evaporated todryness and MeOH (50 mL) was added and evaporated to dryness to removeresidual HCl gas to give(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (1.60 g, 90% yield) as an off white solid (hygroscopic).

Step 7: To a stirred solution of(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (40 mg, 0.10 mmol) in anhydrous DMF (1 mL) was added HOBt (16 mg,0.11 mmol), DIEA (0.07 mL, 0.42 mmol) and EDC (22 mg, 0.11 mmol) atambient temperature. The reaction mixture was stirred for 30 min atambient temperature.(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (26 mg, 0.12 mmol) was added to the reaction mixture andstirred overnight. The solution was evaporated to dryness and theresidue was partitioned with EtOAc (10 mL) and 10% KHSO₄ (5 mL). Theorganic layer was separated and washed with sat. NaHCO₃ solution (10ml), dried over anhydrous Na₂SO₄ and cone under vacuum. The crudereaction mixture was purified by chromatography using MeOH—CH₂Cl₂ toafford tert-butyl(2R,4S)-4-([11,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(48 mg, 80% yield) as a white solid.

Step 8: To tert-butyl(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(48 mg, 0.08 mmol) was added a solution of MeOH—HCl (2.0 mL, 2 M) withstirring at ambient temperature while monitoring for the consumption ofstarting material (30 min to 1h). The solution was evaporated to drynessand MeOH (10 mL) was added and evaporated to dryness to remove residualHCl gas to yield(2R,4S)-4-([1,1′-biphenyl]-3-ylmethyl)-N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedihydrochloride (48 mg, 95%) as a white solid.

Example 210. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethoxybenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1407)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (619mg, 85% yield) was synthesized from 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (500 mg, 1.56 mmol) and3,5-dimethoxybenzyl bromide according to the procedure for compound(1304), step 1.

Step 2: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylatewas synthesized from 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)-5-oxopyrrolidine-1,2-dicarboxylate (619mg, 1.32 mmol) according to the procedure for compound (1304), step 2.

Step 3: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)pyrrolidine-1,2-dicarboxylate (322 mg,54% for 2 steps) was synthesized from 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylateaccording to the procedure for compound (1304), step 3.

Step 4:(2R,4S)-1-(tert-butoxycarbonyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-2-carboxylicacid (232 mg, 90% yield) was synthesized from 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3,5-dimethoxybenzyl)pyrrolidine-1,2-dicarboxylate (322 mg,0.71 mmol) according to the procedure for compound (1304), step 4.

Step 5: tert-Butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-1-carboxylate(61 mg, 76% yield) was synthesized from(2R,4S)-1-(tert-butoxycarbonyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-2-carboxylicacid (53 mg, 0.15 mmol) according to the procedure for compound (1304),step 5.

Step 6: Deprotection of tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-1-carboxylate(61 mg, 0.11 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 211. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-2-carboxamideHydrochloride (1408)

Step 1: A 20 mL pressure vial was charged with 2-benzyl 1-(tert-butyl)(2R,4S)-4-(2-bromobenzyl)pyrrolidine-1,2-dicarboxylate (121 mg, 0.26mmol), (5-chlorothiophen-2-yl)boronic acid (83 mg, 0.51 mmol),Pd(dppf)Cl₂ (19 mg, 0.026 mmol) and K₂CO₃ (108 mg, 0.78 mmol) beforebeing sparged with Ar. Dioxane (3 mL) and H₂O (0.3 mL) were added bysyringe, and the reaction mixture was sealed and allowed to stir at 90°C. for 18 h. Upon completion, the reaction mixture was concentrated andpurified by chromatography (0-30% EtOAc/hexanes) to yield 2-benzyl1-(tert-butyl)(2R,4S)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-1,2-dicarboxylate(82 mg, 62% yield) as a yellow oil.

Step 2: A 50 mL round bottom flask was charged with 2-benzyl1-(tert-butyl)(2R,4S)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-1,2-dicarboxylate(82 mg, 0.16 mmol), LiOH (58 mg, 2.4 mmol) and a mixture of THF/MeOH/H₂O(2:1:1). Upon completion, the reaction mixture was concentrated,acidified to pH ˜3 with 1 M HCl and extracted with EtOAc 2×.Concentration in vacuo gave(2R,4S)-1-(tert-butoxycarbonyl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-2-carboxylicacid as a yellow oil.

Step 3:(2R,4S)-1-(tert-Butoxycarbonyl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-2-carboxylic(17 mg, 0.04 mmol) and HOBt (5.9 mg, 0.044 mmol) were dissolved in DMF(1 mL). EDC (8.4 mg, 0.044 mmol) was then added in a single portion,followed by ethylamine (2 M in THF, 150 μL) and DIEA (21 μL, 0.12 mmol).The resulting solution was allowed to stir at room temp for 16 h. Thereaction mixture was then diluted with EtOAc, washed with 10% aqueousKHSO₄ and brine. Purification by chromatography (70-80% EtOAc/hexanes)gave tert-butyl(2R,4S)-2-(((S)-1-((5-chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-1-carboxylateas a colorless oil.

Step 4: The title compound was synthesized as an off-white powder (10mg, 46% yield over two steps) according to step 4 of the procedure forcompound (1313), except with purification by chromatography (5%MeOH/CH₂Cl₂ containing 2.5% 7 N NH₃-MeOH) followed by treatment with 1 NHCl and lyophilization overnight.

Example 212. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-2-carboxamideTrifluoroacetate (1409)

Steps 1-2: The title compound was synthesized as a beige powder (10 mg,43% yield over two steps) according to steps 3-4 of the procedure forcompound (1408) except with purification by prep-HPLC (ACN/H₂O+TFA).

Example 213. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2-(5-chlorothiophen-2-yl)benzyl)pyrrolidine-2-carboxamideTrifluoroacetate (1410)

Steps 1-2: The title compound was synthesized as a beige powder (7.6 mg,37% yield over two steps) according to steps 3-4 of the procedure forcompound (1408) except with purification by prep-HPLC (ACN/H₂O+TFA).

Example 214. Preparation of3-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)propanoicacid Trifluoroacetate salt (1411)

Steps 1 and 2: To a stirred solution of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidedihydrochloride (10 mg, 0.021 mmol) in CH₂Cl₂ (2 mL) and NEt₃ (0.1 mL)was added ethyl 3-bromopropanoate (0.026 ml, 0.21 mmol) under Aratmosphere. After stirring for 24 h at ambient temperature the reactionmixture was concentrated and dissolved in THF (2 mL). To the solutionwas added LiOH (10 mg, 0.21 mmol) dissolved in 2 ml of water at roomtemperature and stirred at ambient temperature for 18 h. The reactionmixture was acidified with TFA and purified by reverse-phase HPLC toyield3-((2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)propanoicacid trifluoroacetate salt (8.0 mg, 81% yield over two steps).

Example 215. Preparation of6-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)hexanoicacid Trifluoroacetate salt (1412)

6-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)hexanoicacid trifluoroacetate salt was synthesized according to the proceduresfor compound (1411) using the corresponding bromoester.

Example 216. Preparation of(2R,4S,5R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzyl-5-ethylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1413)

To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzyl-5-oxopyrrolidine-1,2-dicarboxylate (0.2 g, 0.49 mmol)in THF (20 mL) at −78° C. was added ethyl magnesium bromide solution(0.53 mL, 0.53 mmol, 1 M in THF) under Ar atmosphere. After 30 min, thereaction mixture was quenched with saturated NaHCO₃ solution (5 mL) andwarmed to 0° C. The organic volatiles were removed under vacuum and theaqueous layer was extracted with CH₂Cl₂ (3×10 mL). The combined organicextracts were thoroughly dried using Na₂SO₄, filtered, and concentratedto afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-benzyl-5-ethyl-5-hydroxypyrrolidine-1,2-dicarboxylate (220 mgcrude). This material was directly used in the next step without furtherpurification. Subsequent steps were followed according to the proceduresfor compound (1304).

Example 217. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamideHydrochloride (1414)

(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1404).

Example 218. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamideHydrochloride (1415)

(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(naphthalen-1-ylmethyl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1334).

Example 219. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethylbenzyl)pyrrolidine-2-carboxamideHydrochloride (1416)

(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethylbenzyl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1404).

Example 220. Preparation of(2R,4R)—N—((S)-1-(((7-Chloro-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1417)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-(((7-chloro-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(102 mg, 92% yield) was synthesized from1-(7-chloro-1H-benzimidazole-5-yl)methanamine (50 mg, 0.28 mmol)according to the procedure for compound (1358), step 2.

Step 2: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((7-chloro-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(102 mg, 0.19 mmol) was conducted according to the procedure forcompound (1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 221. Preparation of(2R,4R)—N—((S)-1-(((7-Chloro-2-methyl-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1418)

Step 1: (7-Chloro-2-methyl-1H-benzo[d]imidazol-5-yl)methanamine wassynthesized from 7-chloro-2-methyl-1H-benzo[d]imidazole-5-carbonitrile(100 mg, 0.52 mmol) according to the procedure for compound (1358), step1.

Step 2: tert-Butyl(2R,4R)-2-(((S)-1-(((7-chloro-2-methyl-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(98 mg, 35% for 2 steps) was synthesized from(7-Chloro-2-methyl-1H-benzo[d]imidazol-5-yl)methanamine (102 mg, 0.52mmol) according to the procedure for compound (1358), step 2.

Step 3: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((7-chloro-2-methyl-1H-benzo[d]imidazol-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(98 mg, 0.18 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 222. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-(3,5-dimethoxybenzyl)pyrrolidine-2-carboxamideTrifluoroacetate salt (1419)

Step 1: tert-Butyl(S)-(1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamate(3.54 g, 76% yield) was synthesized from5-chloro-2-(1H-tetrazole-1-yl)benzenemethamine (3.0 g, 12.2 mmol)according to the procedure for compound (1259), step 3.

Step 2: Deprotection of tert-butyl(S)-(1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamate(3.54 g, 9.3 mmol) was conducted according to the procedure for compound(1259), step 2.

Step 3: tert-Butyl(2R,4S)-2-(((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-1-carboxylate(85 mg, 76% yield) was synthesized from(S)-2-amino-N-(5-chloro-2-(1H-tetrazol-1-yl)benzyl)propenamidetrifluoroacetate salt (99 mg, 0.23 mmol) according to the procedure forcompound (1358), step 2.

Step 4: Deprotection of tert-butyl(2R,4S)-2-(((S)-1-((5-chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3,5-dimethoxybenzyl)pyrrolidine-1-carboxylate(85 mg, 0.14 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 223. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(azetidine-1-carbonyl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1420)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromobenzyl)pyrrolidine-1,2-dicarboxylate was synthesizedaccording to the procedures for compound (1304), step 1 to step 3.

Step 2: A 25 mL vial equipped with a stir bar was charged with(CO₂H.H₂O)₂ (80 mg, 0.63 mmol), Pd(OAc)₂ (1 mg, 0.0042), xantphos (2.5mg, 0.0042), benzyl (2R,4S)-4-(3-bromobenzyl)pyrrolidine-2-carboxylate(200 mg, 0.42 mmol), Ac₂O (60 μL, 0.633 mmol), DIEA (0.11 mL, 0.63mmol), and DMF (2.0 mL) in air. The tube was quickly sealed with aTeflon® high pressure valve, frozen in liquid nitrogen, evacuated andbackfilled with N₂ (5 times). After the reaction mixture was stirred ina preheated oil bath (100° C.) for 6 h, it was allowed to cool down toambient temperature. The reaction mixture was diluted with EtOAc (10mL), acidified with 2 M HCl (5 mL, once), and washed with brine (5 mL,twice). The organic phase was dried over anhydrous Na₂SO₄ andconcentrated in vacuo to afford3-(((3S,5R)-5-((benzyloxy)carbonyl)pyrrolidin-3-yl)methyl)benzoic acid(45 mg, 25% yield) that was directly used in the next step withoutfurther purification.

Step 3: To a stirred solution of3-(((3S,5R)-5-((benzyloxy)carbonyl)pyrrolidin-3-yl)methyl)benzoic acid(45 mg, 0.10 mmol) and triethylamine (0.10 mL, 0.70 mmol) in CH₂Cl₂ (1mL) at 0° C. was added oxalyl chloride (0.34 μL, 0.40 mmol), azetidine(30 mg, 0.50 mmol) followed by DMF (2 drops) under Ar atm. The reactionmixture was stirred at ambient temperature overnight and the solventswere removed under reduced pressure. The residue was purified bychromatography (EtOAc-hexanes) to afford benzyl(2R,4S)-4-(3-(azetidine-1-carbonyl)benzyl)pyrrolidine-2-carboxylate (31mg, 61% yield).

Step 4:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-(azetidine-1-carbonyl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), step 4 to step 8, except that the final product waspurified using reverse-phase HPLC.

Example 224. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-bromoisoxazol-5-yl)methyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1421)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-bromoisoxazol-5-yl)methyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328), except that the final product was purified usingreverse-phase HPLC.

Example 225. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,4-dichlorobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1422)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,4-dichlorobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except that the benzyl deprotection (Step 4) was done byfollowing LiOH conditions as described for compound (1399).

Example 226. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-fluoronaphthalen-1-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1423)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-fluoronaphthalen-1-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 227. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-bis(trifluoromethyl)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1424)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-bis(trifluoromethyl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304), except for the final Boc deprotection:

To tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3,5-bis(trifluoromethyl)benzyl)pyrrolidine-1-carboxylate(27.7 mg, 0.04 mmol) in CH₂Cl₂ (200 p L, 0.2 M) was added TFA (67 p L,0.88 mmol) with stirring at ambient temperature while monitoring for theconsumption of starting material (1-2 h). The solution was evaporated todryness and was purified using reverse-phase HPLC to yield(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-bis(trifluoromethyl)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt (12.8 mg, 39% yield) as a white solid.

Example 228. Preparation of(2R,4R)—N—((S)-1-(((3-Amino-1H-indazol-6-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1425)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-(((3-amino-1H-indazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(147 mg, 88% yield) was synthesized from6-(aminomethyl)-1H-indazol-3-amine (70 mg, 0.43 mmol) according to theprocedure for compound (1358), step 2.

Step 2: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((3-amino-1H-indazol-6-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(147 mg, 0.29 mmol) was conducted according to the procedure forcompound (1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 229. Preparation of(2R,4S)—N—((S)-1-((5-Chloro-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideTrifluoroacetate (1426)

Steps 1-2: The title compound was synthesized as a white powder (11 mg,16% yield over two steps) according to steps 1-2 of the procedure forcompound (1246) using the appropriate starting materials, except withpurification by prep-HPLC (ACN/H₂O+TFA).

Example 230. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1427)

Step 1:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)pyrrolidine-2-carboxamidewas synthesized according to the procedure for compound (1304) (30%yield in 3 steps).

Step 2: A solution of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)pyrrolidine-2-carboxamide(503.3 mg, 1.06 mmol) in THF (11 mL) and water (1.1 mL) was treated withpotassium benzyltrifluoroborate (287.0 mg, 1.45 mmol), CsCO₃ (1.05 g,3.22 mmol), and PdCl₂(pddf) (78 mg, 0.11 mmol). After purging with N₂,the reaction was heated at 90° C. for 16 h and quenched with water. Thereaction mixture was extracted with EtOAc (3 times). The organic layerswere combined, washed with brine, dried (Na₂SO₄), vacuum filtered, andevaporated under vacuum. The crude product was dissolved in CH₂Cl₂ andadsorbed on silica gel. Purification by chromatography (0-100%EtOAc-hexanes) afforded 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-benzylbenzyl)pyrrolidine-1,2-dicarboxylate (425.8 mg, 83%yield).

Step 3: Deprotection of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-benzylbenzyl)pyrrolidine-1,2-dicarboxylate according to theprocedure for compound (1304), step 4 afforded the crude(2R,4S)-4-(4-benzylbenzyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid.

Step 4: tert-Butyl(S)-(1-(((6-((tert-butoxycarbonyl)amino)-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamatewas obtained according to the procedure for compound (1304), step 5 (87%yield).

Step 5: Deprotection of tert-butyl(S)-(1-(((6-((tert-butoxycarbonyl)amino)-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamatewas done according to the procedure for compound (1304), step 6 exceptthe crude product was purified by chromatography (0-10% 7 N NH₃ inMeOH—CH₂Cl₂) afforded(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamide (92%yield).

Step 6: (S)-2-Amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidewas coupled with the crude(2R,4S)-4-(4-benzylbenzyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid according to the procedure for compound 1119, step 1 to affordtert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(4-benzylbenzyl)pyrrolidine-1-carboxylate.

Step 7: A solution of tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(4-benzylbenzyl)pyrrolidine-1-carboxylate(45.0 mg, 0.0768 mmol) in CH₂Cl₂ (1.0 mL) and TES (50 μL) was treatedwith TFA (500 μL) at 0° C. The reaction was stirred at room temp for 2 hand concentrated under reduced pressure. The crude product was dissolvedin CH₂Cl₂ and adsorbed on silica gel. Purification by chromatography(0-5% 7 N NH₃ in MeOH—CH₂Cl₂) afforded(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-benzylbenzyl)pyrrolidine-2-carboxamide(33.0 mg, 88% yield).

Step 8:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-benzylbenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was formed according to the procedure forcompound (1368), step 2.

Example 231. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyanobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1428)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-cyanobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1424).

Example 232. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-cyanobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1429)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-cyanobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1424).

Example 233. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-phenoxybenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1430)

(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-phenoxybenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1424).

Example 234. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-cyanonaphthalen-1-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1431)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-cyanonaphthalen-1-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 235. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-chloronaphthalen-1-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1432)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-chloronaphthalen-1-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except that the benzyl deprotection (Step 4) was done byfollowing LiOH conditions as described in compound (1399).

Example 236. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamide(1433)

Step 1: To a solution of(2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpiperidine-2-carboxylic acid(5.0 g, 16.4 mmol) in MeCN (300 mL, 0.05 M) was added HOBt (2.g, 3.77mmol), DIEA (11.4 mL, 13.7 mmol), and EDC (2.8 g, 3.77 mmol). Afterstirring for 30 min at ambient temperature, benzyl L-alaninehydrochloride (814 mg, 18 mmol) was added and stirred for 16 h. Thereaction mixture was conc and the residue was partitioned with EtOAc and10% KHSO₄ solution. The organic layer was separated and washed with H₂Oand sat. aq NaHCO₃. The organic layer was dried over anhyd Na₂SO₄ andcone under vacuum. The residue was purified by chromatography (0-20%EtOAc-hexanes) to give tert-butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(2.59 mg, 34% yield).

Step 2: A solution of tert-butyl(2R,4S)-2-(((S)-1-(benzyloxy)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(2.59 mg, 5.54 mmol) was degassed with a stream of argon for 2 min. 10%Pd/C (130 mg) was added and a vacuum was pulled for 1 min. A balloon ofH₂ was added and the reaction was monitored for the consumption ofstarting material for 1.5 h. The catalyst was removed by filtration andthe solution was evaporated to give((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpiperidine-2-carbonyl)-L-alanine(1.8 g, 86% yield).

Step 3: tert-Butyl(2R,4S)-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(75 mg, 93% yield) was synthesized from(3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methanamine dihydrochloride (50mg, 0.2 mmol) and((2R,4S)-1-(tert-butoxycarbonyl)-4-phenylpiperidine-2-carbonyl)-L-alanine(57 mg, 0.15 mmol) according to the procedure for compound (1358), step2

Step 4: Deprotection of tert-butyl(2R,4S)-2-(((S)-1-(((3-chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidine-1-carboxylate(75 mg, 0.14 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 237. Preparation of(2R,4R)—N—((S)-1-((Imidazo[1,2-a]pyridin-6-ylmethyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1434)

Step 1:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to imidazo[1,2-a]pyridin-6-ylmethanamine dihydrochlorideaccording to the procedure for (1280), step 4 to give tert-butyl(2R,4R)-2-(((S)-1-((imidazo[1,2-a]pyridin-6-ylmethyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(80 mg, 74% yield).

Step 2: tert-Butyl(2R,4R)-2-(((S)-1-((imidazo[1,2-a]pyridin-6-ylmethyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure for compound (1323), step 3to give(2R,4R)—N—((S)-1-((imidazo[1,2-a]pyridin-6-ylmethyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (86 mg, quant. yield).

Example 238. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-dichlorobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1435)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3,5-dichlorobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1328).

Example 239. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-((5-bromo-3-methyl-2-(1H-tetrazol-1-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideTrifluoroacetate (1436) and(2R,4S)-4-Benzyl-N—((S)-1-((3-methyl-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamide(1437)

Step 1: A 100 mL round bottom flask was charged with5-bromo-2-fluoro-3-methylbenzonitrile (428 mg, 2 mmol), 1H-tetrazole(0.45 M in CAN; 5 mL), K₂CO₃ (318 mg, 2.3 mmol), and DMF (15 mL), thensealed under Ar and stirred at 80° C. for 72 h. Reaction mixture wasthen diluted with EtOAc, washed with H₂O, 5% aq. LiCl and brine. Theorganic layer was dried over Na₂SO₄, concentrated and purified bychromatography (20-60% EtOAc/hexanes) to give5-bromo-3-methyl-2-(2H-tetrazol-2-yl)benzonitrile as a white solid (78mg, 80% yield based on recovered starting material).

Step 2: A solution of 5-bromo-3-methyl-2-(2H-tetrazol-2-yl)benzonitrile(49 mg, 0.19 mmol) in 7 M NH₃ in MeOH (5 mL) was degassed with an Arballoon. Raney nickel (˜40 mg) was added and a vacuum was pulled for 0.5min prior to backfilling with a balloon of H₂. The reaction mixture wasstirred for 16 h at ambient temperature. Upon completion, the catalystwas removed by filtration through diatomaceous earth and the solutionconcentrated in vacuo to give an inseparable mixture of(5-bromo-3-methyl-2-(2H-tetrazol-2-yl)phenyl)methanamine and(3-methyl-2-(2H-tetrazol-2-yl)phenyl)methanamine.

Step 3: DCC-mediated coupling was accomplished according to step 3 ofthe procedure for compound (1313) using the appropriate startingmaterials. Purification by chromatography (EtOAc/hexanes) furnished bothtert-butyl(2R,4S)-4-benzyl-2-(((S)-1-((5-bromo-3-methyl-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(44 mg, 35% yield) and tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-((3-methyl-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(66 mg, 60% yield).

Step 4: Removal of the Boc group from tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-((5-bromo-3-methyl-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylatewas achieved using procedure from step 4 for compound (1313) except withpurification by prep-HPLC (ACN/H₂O+TFA) to yield the title compound as abeige powder (7 mg, 19% yield).

Step 4: Removal of the Boc group from tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-((3-methyl-2-(2H-tetrazol-2-yl)benzyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylatewas achieved using procedure from step 4 for compound (1313) except withpurification by prep HPLC (ACN/H₂O+TFA) to yield the title compound as awhite powder (7 mg, 13% yield).

Example 240. Preparation of(S)—N-((6-Amino-2-methylpyridin-3-yl)methyl)-1-((2R,4S)-4-(4-bromobenzyl)pyrrolidine-2-carbonyl)azetidine-2-carboxamideDi-trifluoroacetate salt (1438)

(S)—N-((6-Amino-2-methylpyridin-3-yl)methyl)-1-((2R,4S)-4-(4-bromobenzyl)pyrrolidine-2-carbonyl)azetidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1451), except that in step 5, a solution of 6 N HCl in iPrOHwas used to deprotect the Boc group and the amide coupling was performedusing HATU.

To (S)—N-((6-amino-2-methylpyridin-3-yl)methyl)azetidine-2-carboxamidehydrochloride (27 mg, 0.11 mmol),(2R,4S)-4-(4-bromobenzyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid (0.11 mmol), DIEA (100 μL, 0.55 mmol) in DMF (370 μL, 0.3 M) wasadded a HATU (63 mg, 0.17 mmol) with stirring at ambient temperaturewhile monitoring for the consumption of starting material (16 h). Thesolution was diluted with EtOAc, extracted with sat. aq NH₄C₁. Theaqueous layer was extracted 2 additional times, then the organic layerwas washed with H₂O, then brine, dried over Na₂SO₄ and evaporated todryness. The resulting residue was purified on an amine column usingEtOAc, then MeOH/CH₂Cl₂ to yield tert-butyl(2R,4S)-2-((S)-2-(((6-amino-2-methylpyridin-3-yl)methyl)carbamoyl)azetidine-1-carbonyl)-4-(4-bromobenzyl)pyrrolidine-1-carboxylate(33 mg, 54% yield) as an off-white film.

Example 241. Preparation of4-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)butanoicacid Trifluoroacetate salt (1439)

4-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)butanoicacid trifluoroacetate salt was synthesized according to the proceduresfor compound (1411) using the corresponding bromoester.

Example 242. Preparation of Ethyl4-((2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)butanoate(1439)

Ethyl4-((2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpiperidin-1-yl)butanoatewas synthesized according to the procedures for compound (1411), step 1,using the corresponding bromoester except that the final product waspurified on an amine column (100% EtOAc).

Example 243. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1-methyl-4-phenylpiperidine-2-carboxamide(1441)

To a stirred solution of(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamidedi-trifluoroacetate salt (100 mg, 0.16 mmol) in CH₂Cl₂ (2 mL) and NEt₃(0.1 mL) was added methyl iodide (0.048 ml, 0.8 mmol) under Aratmosphere. After stirring for 18 h at ambient temperature the reactionmixture was concentrated and purified on an amine column (100% EtOAc) toyield(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1-methyl-4-phenylpiperidine-2-carboxamide(22 mg, 34% yield).

Example 244. Preparation of(2R,4R)—N—((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDihydrochloride (1441)

Step 1: A solution of 3-chloro-1H-pyrrolo[2,3-b]pyridine-5-carbonitrile(215 mg, 1.21 mmol; described for compound (1329)) in anhyd DMF (7 mL)was added to an ice-cold suspension of NaH (60% in oil; 538 mg, 13.4mmol) in anhyd DMF (2 mL) under Ar. The mixture was allowed to warm toambient temperature. After stirring for 30 min, the mixture was cooledover an ice bath and iodomethane (0.22 μl, 3.5 mmol) was added over 5min. The mixture was slowly warmed to ambient temperature, stirred 3 h,then cooled over an ice bath. The reaction was quenched with H₂O thenEtOAc was added. The layers were separated. The aq layer was extractedwith EtOAc and the combined organics were washed with brine, dried(Na₂SO₄) and conc in vacuo. Purification by chromatography (10-35%EtOAc-hexanes) gave3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridine-5-carbonitrile (226 mg, 97%yield).

Steps 2-3: 3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridine-5-carbonitrilewas reduced using the two-step procedure described for compound (1329))to give (3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methanaminedihydrochloride (75 mg, 54% for two steps).

Step 4:((2R,4R)-1-(tert-Butoxycarbonyl)-4-phenylpyrrolidine-2-carbonyl)-L-alaninewas coupled to(3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methanaminedihydrochloride following the procedure given for (1280), step 4 to givetert-butyl(2R,4R)-2-(((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(35 mg, 64% yield).

Step 5: tert-Butyl(2R,4R)-2-(((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylatewas deprotected according to the procedure given for compound (1323),step 3 to give(2R,4R)—N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedihydrochloride (30.9 mg, 93% yield).

Example 245. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2,4-dichlorobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1443)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2,4-dichlorobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1328).

Example 246. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2,5-dichlorobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1444)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(2,5-dichlorobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1328).

Example 247. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromophenoxy)pyrrolidine-2-carboxamideDihydrochloride (1445)

Step 1: To a stirred solution of 2-benzyl 1-(tert-butyl)(2R,4R)-4-hydroxypyrrolidine-1,2-dicarboxylate (410 mg, 1.27 mmol),4-bromophenol (242 mg, 1.39 mmol) and TPP (367 mg, 1.39 mmol) in THF(6.35 mL) was added DIAD (0.27 mL, 1.39 mmol) at ambient temperatureunder Ar. The mixture was stirred at ambient temperature overnight.After removal of the solvent, the resulting residue was purified bychromatography using EtOAc-hexanes to afford 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromophenoxy)pyrrolidine-1,2-dicarboxylate (533 mg, 88%yield) as a colorless solid.

Step 2:(2R,4S)-4-(4-Bromophenoxy)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid was synthesized from 2-benzyl 1-(tert-butyl)(2R,4S)-4-(4-bromophenoxy)pyrrolidine-1,2-dicarboxylate according to theprocedures for compound (1328), step 1.

Step 3:(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromophenoxy)pyrrolidine-2-carboxamidedihydrochloride was synthesized from(2R,4S)-4-(4-bromophenoxy)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid according to the procedures for compound (1304), step 7 and step 8.

Example 248. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenoxypyrrolidine-2-carboxamideDihydrochloride (1446)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenoxypyrrolidine-2-carboxamidedihydrochloride was synthesized from(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromophenoxy)pyrrolidine-2-carboxamidedihydrochloride according to the procedures for compound (1304), step 4.

Example 249. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-fluorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1447)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-fluorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304).

Example 250. Preparation of(2R,4S)-4-benzyl-N—((S)-1-((3,5-dichloro-2-hydroxybenzyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamide,hydrochloride (1448)

Steps 1-2: The title compound was synthesized according to steps 1-2 ofthe procedure for compound (1246) using the appropriate startingmaterials, except with purification by column (MeOH/CH₂Cl₂ containing2.5% 7 N NH₃-MeOH), then treatment with 1 M HCl and lyophilization (10mg, 19% yield over two steps).

Example 251. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1449)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-1,2-dicarboxylatewas synthesized according to the procedure for compound (1304).

Step 2: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-1,2-dicarboxylate(141.4 mg, 0.311 mmol) in THF (7.2 mL) and MeOH (3.6 mL) was added water(3.6 mL) followed by the addition of LiOH (117.0 mg, 4.89 mmol). Afterpurging with N₂, the reaction was stirred at room temp for 16 h, dilutedwith water, and washed with EtOAc. The organic layer was discarded. Theaqueous layer was adjusted to pH 3 with the slow addition of 1 M KHSO₄solution and extracted with EtOAc (3 times). The organic layers werecombined, washed with 5% NaHCO₃ solution, washed with brine, dried(Na₂SO₄), vacuum filtered, and evaporated under vacuum to afford thecrude(2R,4S)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid.

Step 3: To the crude(2R,4S)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylicacid in DMF (5.2 mL) was added NHS (45.0 mg, 0.391 mmol) and DCC (72.0mg, 0.349 mmol). After purging with N₂, the reaction was stirred at roomtemp for 45 min and(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamide (81.0mg, 0.389 mmol) was added. The reaction was stirred at room temp for 16h and evaporated under reduced pressure to dryness. The crude productwas dissolved in CH₂Cl₂ and adsorbed onto silica gel. Purification bychromatography (0-10% MeOH—CH₂Cl₂) afforded tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-1-carboxylate.

Step 4: Deprotection of tert-butyl(2R,4S)-2-(((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-1-carboxylateaccording to the procedure for compound (1427), step 7 exceptpurification by reverse phase HPLC (5-75% MeCN—H₂O) afforded(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[c][1,2,5]thiadiazol-5-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt.

Example 252. Preparation of(2R,4S)-4-Benzyl-N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideDihydrochloride (1450)

Step 1: To a solution of((2R,4S)-4-benzylpyrrolidine-2-carbonyl)-L-alanine (70.2 mg, 0.187 mmol)and NHS (25 mg, 0.22 mmol) in CH₂Cl₂ (3.5 mL) was added DCC (24 mg, 0.12mmol). After stirring for 30 min, a mixture of(3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methanaminedihydrochloride (55 mg, 0.24 mmol) in CH₂Cl₂ (2 mL) and sat. NaHCO₃ (3mL) was added to the reaction mixture. After stirring for 30 min, thereaction was diluted with 5% MeOH—CH₂Cl₂ and washed with sat. NaHCO₃ 3×,dried (Na₂SO₄) and cone in vacuo. Purification (0-10% MeOH—CH₂Cl₂; then50-100% EtOAc-hexanes) gave tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(67.8 mg, 66% yield).

Step 2: To a solution of tert-butyl(2R,4S)-4-benzyl-2-(((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)pyrrolidine-1-carboxylate(66 mg, 0.12 mmol) in MeOH (2 mL) was added 3 M HCl-MeOH (5 mL). Themixture was stirred for 2 h then 6-7 M HCl-iPrOH (3 mL) was added. Afterstirring for 45 min, the reaction mixture was cone in vacuo. The residuewas dissolved in MeCN—H₂O, filtered (0.2 μm syringe filter) andlyophilized to give(2R,4S)-4-benzyl-N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamidedihydrochloride (55 mg, 85% yield).

Example 253. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromo-4-chlorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1451)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromo-4-chlorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1424), except that in step 4, the ester was deprotectedfollowing the procedure below. Additionally, the title compound was notpurified by prep HPLC.

To 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-bromo-4-chlorobenzyl)pyrrolidine-1,2-dicarboxylate (50 mg,0.1 mmol) in THF (2 mL, 0.05 M), MeOH (1 mL, 0.1 M), H₂O (1 mL, 0.1 M)was added a LiOH—H₂O (66 mg, 1.5 mmol) with stirring at ambienttemperature while monitoring for the consumption of starting material(16 h). The solution was brought to pH 3 with 1 N HCl, extracted 3× withEtOAc then dried over Na₂SO₄ and evaporated to dryness. The resultingresidue was carried forward without further purification.

Example 254. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromobenzyl)pyrrolidine-2-carboxamideDihydrochloride (1452)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromobenzyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1328).

Example 255. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((6-methoxynaphthalen-2-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1453)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((6-methoxynaphthalen-2-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 256. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1454)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except that the benzyl deprotection (Step 4) was done byfollowing LiOH conditions as described for compound (1399).

Example 257. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-(trifluoromethoxy)benzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1455)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-(trifluoromethoxy)benzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328).

Example 258. Preparation of(2R,4R)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1456)

(2R,4R)—N—((S)-1-((5-Chloro-2-hydroxy-3-methylbenzyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except(S)-2-amino-N-(5-chloro-2-hydroxy-3-methylbenzyl)propenamide was used instep 7 and the benzyl deprotection (Step 4) was done by following LiOHconditions as described for compound (1399).

Example 259. Preparation of(2R,4R)—N—((S)-1-(((5-chloroquinolin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(1457)

Steps 1-2: The title compound was synthesized as a beige powderaccording to steps 3-4 of the procedure for compound 1119 using theappropriate starting materials (8.1 mg, 12% yield over two steps).

Example 260. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[b]thiophen-2-ylmethyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1458)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[b]thiophen-2-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1451).

Example 261. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1459)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328).

Example 262. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorobenzo[d]thiazol-2-yl)methyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1460)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorobenzo[d]thiazol-2-yl)methyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328), except that the final product was purified usingreverse-phase HPLC.

Example 263. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-3-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1461)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((5-chlorothiophen-3-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304), except that the benzyl deprotection (Step 4) was done byfollowing LiOH conditions as described for compound (1399).

Example 264. Preparation of(2R,4R)—N—((S)-1-(((5-bromo-1H-indazol-7-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamide(1462)

Step 1: (5-Bromo-1H-indazol-7-yl)methanol (62 mg, 0.2 mmol) wasdissolved in CH₂Cl₂ (2 mL) and treated with PBr₃ (20 μL, 0.21 mmol),then stirred at ambient temperature overnight. The reaction mixture wasdiluted with CH₂Cl₂ and washed with H₂O and brine, then dried overNa₂SO₄ and concentrated to furnish 5-bromo-7-(bromomethyl)-1H-indazoleas a white solid (58 mg, quant. yield).

Step 2: A 50 mL round bottom flask was charged with5-bromo-7-(bromomethyl)-1H-indazole (58 mg, 0.2 mmol), potassiumphthalimide (37 mg, 0.2 mmol) and DMF (2 mL), then stirred at ambienttemperature overnight. Upon completion, the reaction mixture wasconcentrated and purified by chromatography to give2-((5-bromo-1H-indazol-7-yl)methyl)isoindoline-1,3-dione as a whitesolid (13 mg, 18% yield).

Step 3: 2-((5-Bromo-1H-indazol-7-yl)methyl)isoindoline-1,3-dione (13 mg,0.04 mmol) was dissolved in EtOH (1 mL) and treated with hydrazinehydrate. After 4 h at ambient temperature, the reaction mixture wasconcentrated, dissolved in 3 N HCl and filtered through a syringe filter(0.2 μm) and concentrated in vacuo to give(5-bromo-1H-indazol-7-yl)methanamine, hydrochloride as a white solid (10mg, quant. yield).

Step 4: The title compound was synthesized as a white solid (6.2 mg, 35%yield over two steps) according to steps 1-2 of the procedure forcompound (1246) using the appropriate starting materials, except withpurification by prep HPLC (ACN/H₂O+TFA).

Example 265. Preparation of(2R,4R)—N—((S)-1-(((1H-Pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1463)

Step 1: tert-Butyl(2R,4R)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(49 mg, 48% yield) was synthesized from(1H-pyrrolo[3,2-c]pyridin-2-yl)methanamine according to the procedurefor compound (1358), step 2.

Step 2: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(49 mg, 0.1 mmol) was conducted according to the procedure for compound(1260), step 4.

Example 266. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromo-4-chlorobenzyl)-1-ethylpyrrolidine-2-carboxamide(1464)

To(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromo-4-chlorobenzyl)pyrrolidine-2-carboxamideditrifluoroacetate (20 mg, 0.027 mmol) in NEt₃ (20 μL, 1.6 M) and CH₂Cl₂(340 μL, 0.08 M) was added ethyl bromide (10 μL, 0.135 mmol) withstirring at ambient temperature while monitoring for the consumption ofstarting material (3 d). The solution was concentrated and evaporated todryness. The resulting residue was purified on an amine column usingEtOAc, then MeOH/CH₂Cl₂ to yield(2R,4S)—N—((S)-1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-bromo-4-chlorobenzyl)-1-ethylpyrrolidine-2-carboxamide(4.6 mg, 32% yield) as an off-white solid.

Example 267. Preparation of(S)—N-((6-Amino-2-methylpyridin-3-yl)methyl)-1-((2R,4S)-4-(4-bromobenzyl)pyrrolidine-2-carbonyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1465)

(S)—N-((6-Amino-2-methylpyridin-3-yl)methyl)-1-((2R,4S)-4-(4-bromobenzyl)pyrrolidine-2-carbonyl)pyrrolidine-2-carboxamideditrifluoroacetate was synthesized according to the procedures forcompound (1438) except that in step 5, DMF was used as the solvent inplace of CH₂Cl₂ for the DCC coupling and TFA (20 eq.) in CH₂Cl₂ (0.2 M)was used to deprotect the Boc group.

Example 268. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromo-3-chlorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1466)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromo-3-chlorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1451).

Example 269. Preparation of(S)—N-(1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzyl-1H-pyrrole-2-carboxamidetrifluoroacetic acid (1467)

To a solution consisting of 4-benzyl-1H-pyrrole-2-carboxylic acid (25mg, 0.13 mmol) and HATU (53 mg, 0.14 mmol) in anhydrous DMF (1 mL) wasadded DIEA (60 μL, 0.34 mmol). The reaction mixture was stirred for 30min at ambient temperature before(S)-2-amino-N-((6-amino-2-methylpyridin-3-yl)methyl)propanamidehydrochloride (28 mg, 0.11 mmol) was added to the reaction mixture andstirred overnight. The reaction mixture was made acidic by adding TFA(100 μL) and the crude reaction mixture purified by reverse-phase HPLCto afford(S)—N-(1-(((6-amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzyl-1H-pyrrole-2-carboxamidetrifluoroacetic acid (17.2 mg, 30%) as a light tan solid.

Example 270. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2-methylpyridin-4-yl)methyl)pyrrolidine-2-carboxamideTrifluoroacetate (1468)

Step 1: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-((2-methylpyridin-4-yl)methyl)-5-oxopyrrolidine-1,2-dicarboxylatewas synthesized according step 1 of the procedure for compound (1304)using the appropriate starting materials (113 mg, 24% yield).

Step 2: 2-Benzyl 1-(tert-butyl)(2R,4S)-5-hydroxy-4-((2-methylpyridin-4-yl)methyl)pyrrolidine-1,2-dicarboxylatewas synthesized as a colorless oil according to step 2 of the procedurefor compound (1304), except the crude product was filtered throughdiatomaceous earth (101 mg, 87% yield).

Step 3: 2-Benzyl 1-(tert-butyl)(2R,4S)-4-((2-methylpyridin-4-yl)methyl)pyrrolidine-1,2-dicarboxylatewas synthesized as a colorless oil according step 3 of the procedure forcompound (1304) (52 mg, 62% yield).

Step 4:(2R,4S)-1-(tert-butoxycarbonyl)-4-((2-methylpyridin-4-yl)methyl)pyrrolidine-2-carboxylicacid was synthesized as a colorless oil according to step 4 of theprocedure for compound (1304) (41 mg, 98% yield).

Steps 5-6: The title compound was synthesized as a light pink solidaccording to steps 5-6 of the procedure for compound (1304), except forpurification by prep HPLC (ACN/H₂O+TFA) (16.8 mg, 40% yield over twosteps).

Example 271. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((2-methylpyridin-4-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1469)

Steps 1-2: The title compound was synthesized as a beige powderaccording to steps 5-6 of the procedure for compound (1304) (15.4 mg,75% yield over two steps).

Example 272. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[c][1,2,5]oxadiazol-5-ylmethyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1470)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(benzo[c][1,2,5]oxadiazol-5-ylmethyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedure forcompound (1449), step 1-4.

Example 273. Preparation of(2R,4R)—N—((S)-1-oxo-1-((Thieno[2,3-b]pyridin-5-ylmethyl)amino)propan-2-yl)-4-phenylpyrrolidine-2-carboxamideTrifluoroacetate salt (1471) (69)

Step 1: Thieno[2,3-b]pyridin-5-ylmethanamine (97 mg, 95% yield) wassynthesized from thieno[2,3-b]pyridine-5-carbonitrile (100 mg, 0.62mmol) according to the procedure for compound (1358), step 1.

Step 2: tert-Butyl(2R,4R)-2-(((S)-1-oxo-1-((thieno[2,3-b]pyridin-5-ylmethyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(120 mg, 91% yield) was synthesized fromthieno[2,3-b]pyridin-5-ylmethanamine (50 mg, 0.34 mmol) according to theprocedure for compound (1358), step 2.

Step 3: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-oxo-1-((thieno[2,3-b]pyridin-5-ylmethyl)amino)propan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(120 mg, 0.29 mmol) was conducted according to the procedure forcompound (1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 274. Preparation of(2R,4S)—N—((S)-1-(((1H-Pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-benzylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1472)

Step 1: tert-Butyl(2R,4S)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(36 mg, 33% yield) was synthesized from(1H-pyrrolo[3,2-c]pyridin-2-yl)methanamine and(2R,4S)-4-benzyl-1-(tert-butoxycarbonyl)pyrrolidine-2-carboxylic acid(80 mg, 0.21 mmol, prepared according to the procedure for compound(1304), step 1-4 according to the procedure for compound (1358), step 2.

Step 2: Deprotection of tert-butyl(2R,4S)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-benzylpyrrolidine-1-carboxylate(36 mg, 0.07 mmol) was conducted according to the procedure for compound(1260), step 4 except that the final product was purified usingreverse-phase HPLC.

Example 275. Preparation of3-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidin-1-yl)propanoicacid Trifluoroacetate salt (1473)

3-((2R,4S)-2-(((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidin-1-yl)propanoicacid was synthesized according to the procedures for compound (1411)using the corresponding bromoester.

Example 276. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamideTrifluoroacetate salt (1474)

(2R,4S)—N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamidetrifluoroacetate salt was synthesized according to the procedures forcompound (1476).

Example 277. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-methoxybenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1475)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-methoxybenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1328).

Example 278. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-methylbenzyl)pyrrolidine-2-carboxamideHydrochloride (1476)

(2R,4S)—N—((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-methylbenzyl)pyrrolidine-2-carboxamidehydrochloride was synthesized according to the procedures for compound(1450).

Example 279. Preparation of(2R,4S)—N—((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chlorobenzyl)pyrrolidine-2-carboxamideTrifluoroacetate salt (1477)

(2R,4S)—N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chlorobenzyl)pyrrolidine-2-carboxamidetrifluoroacetate salt was synthesized according to the procedures forcompound (1450).

Example 280. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-methoxynaphthalen-2-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1478)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((3-methoxynaphthalen-2-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 281. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-methylnaphthalen-1-yl)methyl)pyrrolidine-2-carboxamideDihydrochloride (1479)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-methylnaphthalen-1-yl)methyl)pyrrolidine-2-carboxamidedihydrochloride was synthesized according to the procedures for compound(1304).

Example 282. Preparation of(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4,4-bis(4-fluorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1480)

(R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4,4-bis(4-fluorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1304).

Example 283. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(1-phenylcyclopropyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1481)

Step 1:(R)-1-(tert-Butoxycarbonyl)-4-(1-phenylcyclopropyl)-2,5-dihydro-1H-pyrrole-2-carboxylicacid was synthesized from 1-(tert-butyl) 2-methyl(R)-4-oxopyrrolidine-1,2-dicarboxylate according to the procedures forcompound (1247), steps 1 to 3, utilizing potassiumtrifluoro(1-phenylcyclopropyl)borate as the coupling partner in thefirst step.

Steps 2-4:(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(1-phenylcyclopropyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1359), steps 2-4.

Example 284. Preparation of(2R,4S)-4-(2-bromobenzyl)-N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride (1482)

(2R,4S)-4-(2-bromobenzyl)-N—((S)-1-(((3-chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)pyrrolidine-2-carboxamideHydrochloride was synthesized according to the procedures for compound(1450).

Example 285. Preparation of(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-bromo-5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1483)

(2R,4R)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-((4-bromo-5-chlorothiophen-2-yl)methyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedure forcompound (1449).

Example 286. Preparation of2-((2R,4S)-2-(((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidin-1-yl)aceticacid Trifluoroacetate salt (1484)

2-((2R,4S)-2-(((S)-1-(((3-Chloro-1-methyl-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidin-1-yl)aceticacid trifluoroacetate salt was synthesized according to the proceduresfor compound (1411).

Example 287. Preparation of(2R,4R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1485)

(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound 6. The firstUVActive material eluting from the column in step 1.

Example 288. Preparation of(2S,4S)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1486)

(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound 6. The secondUVActive material eluting from the column in step 1.

Example 289. Preparation of(2S,4R)—N—((S)-1-((4-carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-phenylpiperidine-2-carboxamideDihydrochloride (1487)

(2R,4R)—N—((S)-1-((4-Carbamimidoylbenzyl)amino)-1-oxopropan-2-yl)-4-(m-tolyl)piperidine-2-carboxamidewas synthesized according to the procedures for compound 6. The fourthUVActive material eluting from the column in step 1.

Example 290. Preparation ofN-(5-Chloro-2-(1H-tetrazol-1-yl)benzyl)-2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetamide(1489)

Step 1: The title compound was prepared according to step 3 of theprocedure for compound (1365), using the appropriate starting materialsexcept with purification by chromatography (95% EtOAc/hexanes; 42 mg,88% yield).

Example 291. Preparation ofN-((3-Chloro-1H-pyrrolo[2,3-b]pyridin-5-yl)methyl)-2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetamideAcetate salt (1490)

Step 1: The title compound was prepare according to step 3 of theprocedure or compound (1365), using the appropriate starting materialsexcept with purification by chromatography (MeOH/CH₂Cl₂+AcOH; 10 mg, 22%yield).

Example 292. Preparation ofN-((1-Aminoisoquinolin-6-yl)methyl)-2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetamideTrifluoroacetamide salt (1491)

Step 1: The title compound was prepared according to step 3 of theprocedure for compound (1365), using the appropriate starting materials(9 mg, 20% yield).

Example 293. Preparation ofN-((2-Amino-1H-benzo[d]imidazol-6-yl)methyl)-2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetamideTrifluoroacetamide salt (1492)

Step 1: A solution of ethyl2-(3-bromo-6-methyl-2-oxopyrazin-1(2H)-yl)acetate (411 mg, 1.5 mmol) andphenethylamine (189 μL, 1.5 mmol) in 1:1 toluene/EtOH (10 mL) was heatedat 125° C. for 18 h in a sealed flask. Upon cooling, the reactionmixture was concentrated then taken up in EtOAc and washed with sat. aq.NaHCO₃, brine and dried over Na₂SO₄ then concentrated. The crude productwas purified by chromatography (60% EtOAc/hexanes) to furnish ethyl2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetate as a beigesolid (390 mg, 82% yield).

Step 2: Ethyl2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetate (390 mg,1.24 mmol) was dissolved in 1:1 THF/MeOH (6 mL) and treated with 1 N aq.NaOH (3 mL). After 2 h, the organic solvents were removed in vacuo andcooled to 0° C. before being acidified with 1 N HCl. The precipitatedproduct was collected by filtration to give2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetic acid as apale yellow powder (285 mg, 81% yield).

Step 3: A 50 mL round bottom flask was charged with2-(6-methyl-2-oxo-3-(phenethylamino)pyrazin-1(2H)-yl)acetic acid (29 mg,0.1 mmol), EDC (21 mg, 0.11 mmol), HOBt (16 mg, 0.12 mmol) and DMF (1mL). After 5 min, 6-(aminomethyl)-1H-benzo[d]imidazol-2-aminedihydrochloride (26 mg, 0.11 mmol) and DIEA (52 μL, 0.3 mmol) were addedand the reaction stirred for 16 h at ambient temperature. Uponcompletion, the reaction mixture was diluted with EtOAc and washed withsat. NaHCO₃ and brine, then dried over Na₂SO₄ and concentrated.Purification by prep-HPLC (ACN/H₂O+TFA) gave the title compound as awhite powder (19 mg, 35% yield).

Example 294. Preparation of(2R,4R)—N—((S)-1-(((4-Bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1493)

Step 1: To a 0° C. solution of methyl4-bromo-1H-pyrrolo[2,3-c]pyridine-2-carboxylate (1.0 g, 3.92 mmol) inTHF (20 mL, 5.1 M) was added lithium aluminum hydride (1 M in THF, 6.3mL, 6.3 mmol). After stirring for 1 h at the same temperature, thereaction was quenched by addition of H₂O. The resulting mixture wasextracted with EtOAc, dried over anhyd Na₂SO₄, and conc under vacuum.The residue was purified by chromatography (0-100% EtOAc-hexanes) togive (4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methanol (206 mg, 23%yield).

Step 2: To a solution of (4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methanol(206 mg, 0.91 mmol) in CH₂Cl₂ (1.5 mL, 0.6 M) was added 4.0 M HCl indioxane (2.2 mL). After stirring for 15 min, the reaction mixture wasconc under vacuum. To this residue was added thionyl chloride (1 mL) at0° C. After stirring for 2 min at reflux, the reaction mixture wasconcentrated to give the crude4-bromo-2-(chloromethyl)-1H-pyrrolo[2,3-c]pyridine hydrochloride salt(256 mg, 99% yield).

Step 3: To a solution of di-tert-butyl iminodicarboxylate (295 mg, 1.36mmol) in DMF (5 mL, 0.27 M) was added sodium hydride (60% dispersion inmineral oil). After stirring for 30 min, the crude4-bromo-2-(chloromethyl)-1H-pyrrolo[2,3-c]pyridine hydrochloride salt(256 mg, 0.9 mmol) in DMF (1.0 mL, 0.9 M) was added drop-wise. Afterstirring for 2 h at room temperature, another 0.5 eq of sodium hydridewas added. After stirring for 16 h at the same temperature, the reactionwas quenched by addition of H₂O. The resulting mixture was extractedwith EtOAc, dried over anhyd Na₂SO₄, and conc under vacuum. The residuewas dissolved in CH₂Cl₂ (5 mL) and 4.0 M HCl in dioxane was added. Afterstirring for 22 h, the reaction mixture was concentrated to the crude(4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methanamine hydrochloride salt(233 mg, 86% yield).

Step 4: tert-Butyl(2R,4R)-2-(((S)-1-(((4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(13 mg, 4% yield) was synthesized from the crude(4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methanamine hydrochloride salt(217 mg, 0.6 mmol) according to the procedure for compound, step 2.

Step 5: Deprotection of tert-butyl(2R,4R)-2-(((S)-1-(((4-bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-phenylpyrrolidine-1-carboxylate(13 mg, 0.02 mmol) was conducted according to the procedure forcompound, step 4 except that the final product was purified usingreverse-phase HPLC.

Example 295. Preparation of(2R,4S)—N—((S)-1-(((1H-Pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamideDi-trifluoroacetate salt (1494)

Step 1: To a −78° C. solution of 2-benzyl 1-(tert-butyl)(R)-5-oxopyrrolidine-1,2-dicarboxylate (500 mg, 1.57 mmol) in THF (10mL, 0.16 M) was slowly added lithium bis(trimethylsilyl)amide (1 M inTHF, 1.72 mL, 1.72 mmol). After stirring for 1 h at the sametemperature, 4-(bromomethyl)-2-chloro-1-fluorobenzene (420 mg, 1.88mmol) in THF (2 mL) was added. After stirring for 2 h at the sametemperature, the reaction was quenched by addition of sat. aq NH₄C₁. Theresulting mixture was extracted with EtOAc, dried over anhyd Na₂SO₄, andconc under vacuum. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate(450 mg, 62% yield).

Step 2: To a −78° C. solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)-5-oxopyrrolidine-1,2-dicarboxylate(450 mg, 0.97 mmol) in THF (7 mL, 0.14 M) was added lithiumtriethylborohydride (1 M in THF, 1.07 mL, 1.07 mmol). After stirring for30 min, the reaction was quenched by addition of sat. aq NaHCO₃ andwarmed to 0° C. 30% H₂O₂(about 8 drops) was added and the reactionmixture was stirred for 30 min at same temperature. The organicvolatiles were removed under vacuum and the aqueous layer was extractedwith CH₂Cl₂. The combined extracts were dried over anhyd Na₂SO₄, andconc under vacuum to give 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate(450 mg, 100%) which was used in the next step without furtherpurification.

Step 3: To a −78° C. solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)-5-hydroxypyrrolidine-1,2-dicarboxylate(450 mg, 0.97 mmol) in CH₂Cl₂ (6 mL, 0.16 M) was added triethylsilane(0.38 mL, 2.13 mmol) and boron trifluoride diethyl etherate (0.65 mL,2.13 mmol). After stirring for 2 h at the same temperature, the reactionwas quenched by addition of sat. aq NaHCO₃ solution. The resultingmixture was extracted with CH₂Cl₂, dried over anhyd Na₂SO₄, and concunder vacuum. The residue was purified by chromatography (0-100%EtOAc-hexanes) to give 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-1,2-dicarboxylate (220mg, 51% yield for two steps).

Step 4: A solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-1,2-dicarboxylate (220mg, 0.49 mmol) was degassed with a stream of Ar for 2 min. 10% Pd/C (10mg) was added and a vacuum was pulled for 1 min. A balloon of H₂ wasadded and the reaction was monitored for the consumption of startingmaterial for 1.5 h. The catalyst was removed by filtration and thesolution was evaporated to give(2R,4S)-1-(tert-butoxycarbonyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxylicacid (175 mg, 100% yield).

Step 5: To a solution of (tert-butoxycarbonyl)-L-alanine (467 mg, 2.47mmol) in CH₂Cl₂ (15 mL) and MeOH (5 mL) was added NHS (313 mg, 2.72mmol) with stirring at room temp until dissolved. DCC (561 mg, 2.72mmol) was added and stirred for 1 h.(1H-pyrrolo[3,2-c]pyridin-2-yl)methanamine (400 mg, 2.72 mmol) was addedto the above mixture and stirred for 1 h. The reaction was quenched byaddition of H₂O and the resulting mixture was extracted with CH₂Cl₂,dried over anhyd Na₂SO₄, and conc under vacuum. The residue was purifiedby chromatography (0-100% EtOAc-hexanes) to give tert-butyl(S)-(1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(129 mg, 15% yield).

Step 6: To a 0° C. solution of tert-butyl(S)-(1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamate(129 mg, 0.4 mmol) in CH₂Cl₂ (10 mL, 0.04 M) was added 20% TFA in CH₂Cl₂(10 mL). After stirring for 3 h at room temperature, the reactionmixture was concentrated to give(S)—N-((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)-2-aminopropanamidedi-trifluoroacetate salt (180 mg, 100% yield).

Step 7: To a solution of 2-benzyl 1-(tert-butyl)(2R,4S)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-1,2-dicarboxylate (25 mg,0.07 mmol) in anhyd DMF (2 mL, 0.04 M) was added HOBt (14 mg, 0.09mmol), DIEA (0.05 mL, 0.28 mmol), and EDC (14 mg, 0.09 mmol). Afterstirring for 30 min at ambient temperature,(S)—N-((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)-2-aminopropanamidedi-trifluoroacetate salt (38 mg, 0.08 mmol) was added and stirred for 16h. The reaction mixture was conc and the residue was partitioned withEtOAc and 10% KHSO₄ solution. The organic layer was separated and washedwith H₂O and sat. aq NaHCO₃. The organic layer was dried over anhydNa₂SO₄ and concd. The residue was purified by chromatography (0-100% [5%7 N NH₃ in MeOH/CH₂Cl₂]—CH₂Cl₂) to give tert-butyl(2R,4S)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-1-carboxylate(27 mg, 68% yield).

Step 8: To a 0° C. solution of tert-butyl(2R,4S)-2-(((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)carbamoyl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-1-carboxylate(27 mg, 0.05 mmol) in CH₂Cl₂ (1 mL, 0.05 M) was added 20% TFA in CH₂Cl₂(1 mL). After stirring for 3 h at room temperature, the reaction mixturewas concentrated to give(2R,4S)—N—((S)-1-(((1H-pyrrolo[3,2-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-(3-chloro-4-fluorobenzyl)pyrrolidine-2-carboxamidedi-trifluoroacetate salt (33 mg, 100% yield).

Example 296. Preparation of(2R,4R)—N—((S)-1-(((1H-Pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1495)

Step 1:(2R,4R)—N—((S)-1-(((1H-Pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedi-trifluoroacetate salt (2.0 mg, 80% yield) was synthesized from(2R,4R)—N—((S)-1-(((4-Bromo-1H-pyrrolo[2,3-c]pyridin-2-yl)methyl)amino)-1-oxopropan-2-yl)-4-phenylpyrrolidine-2-carboxamidedi-trifluoroacetate salt (prepared according to the procedure forcompound (1493), step 1-5) according to the procedure for compound(1264), step 2.

Example 297. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1-ethyl-4-phenylpiperidine-2-carboxamide(1496)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-1-ethyl-4-phenylpiperidine-2-carboxamidewas synthesized according to the procedures for compound (1464).

Example 298. Preparation of(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)-N-methylpyrrolidine-2-carboxamideDi-trifluoroacetate salt (1497)

(2R,4S)—N—((S)-1-(((6-Amino-2-methylpyridin-3-yl)methyl)amino)-1-oxopropan-2-yl)-4-(4-bromobenzyl)-N-methylpyrrolidine-2-carboxamidedi-trifluoroacetate salt was synthesized according to the procedures forcompound (1438), except that the title compound was not purified by prepHPLC.

Example 299. Preparation of2-(Pyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamide Dihydrochloride(2001)

This method is a modification of the general procedure of W. B. Young etal., Bioorg. Med. Chem. Lett. 16 (2006) 710-713. A mixture of3,4-diaminobenzimidamide HCl (0.5 g, 2.6 mmol), picolinaldehyde (0.22mL, 2.3 mmol), benzoquinone (0.28 g, 2.6 mmol) and ethanol (15 mL) washeated at reflux. After stirring for 3 h, the mixture was allowed towarm to room temp and the volatiles removed under reduced pressure. Theresidue was dissolved in methanol (5 mL) then added to cold MeCN (100mL) while stirring to yield a precipitate that was isolated byfiltration. The precipitate was dissolved in 6 N HCl (20 mL) and pouredinto stirring acetone (150 mL) to give a precipitate. The precipitatewas isolated by filtration, washed with acetone and dried under reducedpressure to provide2-(pyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamide, dihydrochloridesalt (0.53 g, 65%).

Proceeding similarly to the procedure for compound 2001, but with theappropriate starting materials, the following compounds were made:2-(1H-imidazol-4-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2000);2-(6-methylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamide;2-(6-methylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamide (2003);2-(3-methylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2004);2-(4-methylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2005);2-(5-ethylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2007);2-(6-ethylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2008);1H,1′H-[2,2′-bibenzo[d]imidazole-5-carboximidamide dihydrochloride(2009); 2-(5-methylpyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2010);2-(6-(methoxymethyl)pyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2011);2-(4-ethoxypyridin-2-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2012);2-(quinolin-2-yl)-1H-benzo[d]imidazole-5-carboximidamide dihydrochloride(2013); 2-(isoquinolin-3-yl)-1H-benzo[d]imidazole-5-carboximidamidedihydrochloride (2014); and2-(6-(4-fluorophenyl)pyridin-2-yl)-benzo[d]imidazole-5-carboximidamidedihydrochloride (2016).

Example 300. Preparation of2-(Pyridin-2-ylmethyl)-1H-benzo[d]imidazole-5-carboximidamideDihydrochloride (2002)

This method is a modification of the general procedure of W. B. Young etal., Bioorg. Med. Chem. Lett. 16 (2006) 710-713. An oven-dried flask wascharged with 3,4-diaminobenzimidamide HCl (0.99 g, 5.3 mmol), ethyl2-(pyridin-2-yl)acetate (0.9 mL, 5.9 mmol) and polyphosphoric acid (8mL). The mixture was heated to 180° C. After stirring for 2 h, themixture was allowed to warm to room temp. The mixture was diluted withH₂O (50 mL) and then cooled over an ice bath. After the mixture wascooled, an aq solution of 50% NaOH was added to adjust the pH to 8, andthe mixture was allowed to warm to room temp. To the gummy mixture wasadded MeOH (10 mL); the volatiles were removed under reduced pressure.Aqueous saturated NaHCO₃ was added with vigorous stirring until aprecipitate was obtained. The precipitate was then isolated byfiltration and rinsed with H₂O. The precipitate was dissolved in 6 N HCl(15 mL). The solution was poured into stirring acetone (150 mL) to givea precipitate, which was isolated by filtration, washed with acetone,and dried to provide2-(pyridin-2-ylmethyl)-1H-benzo[d]imidazole-5-carboximidamide,dihydrochloride salt (0.24 g, 14%).

Example 301. Preparation of2-((1H-Benzo[d]imidazol-2-yl)methyl)-1H-benzo[d]imidazole-5-carboximidamideDihydrochloride (2015)

This method is a modification of the general procedure of W. B. Young etal., Bioorg. Med. Chem. Lett. 16 (2006) 710-713. An oven-dried flask wascharged with 3,4-diaminobenzimidamide HCl (0.98 g, 5.2 mmol), ethyl2-(1H-benzo[d]imidazol-2-yl)acetate (1.2 g, 5.8 mmol) and polyphosphoricacid (8 mL). The mixture was heated to 185° C. After stirring for 2 h,the mixture was allowed to cool to room temp. After 8 h, the mixture wasdiluted with H₂O (50 mL) and then cooled over an ice bath. After themixture was cooled, a solution of 50% NaOH was added to adjust the pH to9. The mixture was vigorously stirred and gradually warmed to room temp;the solids were isolated by vacuum filtration and rinsed with H₂O. Thesolids were then stirred for 30 min with saturated aq NaHCO₃, filtered,and rinsed with H₂O. The precipitate was collected and dissolved in 6 NHCl (15 mL). The solution was poured into stirring acetone (150 mL) togive a precipitate. The precipitate was isolated by filtration, washedwith acetone and dried to provide2-((1H-benzo[d]imidazol-2-yl)methyl)-1H-benzo[d]imidazole-5-carboximidamide,dihydrochloride salt (1.6 g, 85%).

Example 302. Preparation of((4-((2-(3-Benzyl-7-carbamoyl-2,4-dioxo-3,4-dihydroquinazolin-1(2H)-yl)acetamido)methyl)phenyl)(imino)methyl)-λ⁵-azaneylAcetate (2017)

Step 1: A reaction vessel was charged with 2-aminoterephthalic acid (600mg, 3.31 mmol) and THF (10 mL). To this was added benzyl isocyanate (485mg, 3.64 mmol), and the mixture was refluxed at 70° C. for 4 h. Thereaction mixture was then cooled, and the solvent was evaporated undervacuum and replaced with EtOH (10 mL). The reaction was treated withH₂SO₄ (2 mL) and stirred at 70° C. for 2 h. Upon completion, thereaction was cooled to 5° C. and treated with water, whereupon a slurrywas formed. The precipitate was filtered and washed with H₂O andhexanes, then collected as an off-white solid that was then re-suspendedin THF (10 mL) and H₂O (10 mL). LiOH (2 equiv, 159 mg) was added in oneportion and the reaction stirred at ambient temperature for 2 h. Aftercompletion, THF was removed under vacuum and the reaction then acidifiedwith 1 N HCl. The resulting slurry was filtered to yield3-benzyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxylic acid as awhite powder (650 mg, 66% yield over 3 steps).

Step 2: A mixture of3-benzyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxylic acid (297mg, 1 mmol), tritylamine (285 mg, 1.1 mmol), Et₃N (418 μL, 3 mmol) inDMF (10 mL) was treated with PyBOP (513 mg, 1.1 mmol). The reactionmixture was allowed to stir at ambient temperature overnight, thendiluted with EtOAc and washed with 10% aq KHSO₄, brine, and saturated aqNaHCO₃. The organic layer was dried over Na₂SO₄, filtered, concentratedunder vacuum, and then purified by chromatography (10-30% EtOAc-hexanes)to yield3-benzyl-2,4-dioxo-N-trityl-1,2,3,4-tetrahydroquinazoline-7-carboxamideas a white crystalline solid (126 mg, 23% yield).

Step 3: A reaction vessel was charged with3-benzyl-2,4-dioxo-N-trityl-1,2,3,4-tetrahydroquinazoline-7-carboxamide(120 mg, 0.22 mmol), K₂CO₃ (76 mg, 0.55 mmol) and DMF (2 mL). To thisstirring solution was added ethyl bromoacetate (28 μL, 0.25 mmol) andthe mixture was allowed to stir at room temp overnight. Upon completion,the reaction mixture was treated with H₂O, whereupon ethyl2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)acetateprecipitated as a white solid (62 mg, quant. yield) which was collectedby filtration.

Step 4: To a stirring suspension of ethyl2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)acetate(137 mg, 0.22 mmol) in THF (2.5 mL) and H₂O (2.5 mL) was added LiOH (11mg, 0.44 mmol) in one portion. The reaction mixture was stirred atambient temp overnight. After completion, the reaction mixture wasneutralized with 10% aq KHSO₄, and extracted with EtOAc (10 mL×3). Thecombined organics were washed with brine, dried (Na₂SO₄), filtered andconcentrated under vacuum to provide2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)aceticacid as a white powder (59 mg, 45% yield).

Step 5: To the reaction vessel was added2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)aceticacid (59 mg, 0.1 mmol), DMAP (24.4 mg, 0.2 mmol) and CH₂Cl₂ (1 mL). Tothis stirring mixture was added EDC (23 mg, 0.12 mmol) followed bybenzyl ((4-(aminomethyl)phenyl)(imino)methyl)carbamate (35.2 mg, 0.11mmol). The reaction mixture was stirred at ambient temp overnight, afterwhich time it was washed successively with 10% aq KHSO₄, H₂O, saturatedaq NaHCO₃, and brine. The organic layer was dried (Na₂SO₄) andconcentrated under vacuum to provide benzyl((4-((2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)acetamido)methyl)phenyl)(imino)methyl)carbamateas a white solid (86 mg, quant. yield).

Step 6: Benzyl((4-((2-(3-benzyl-2,4-dioxo-7-(tritylcarbamoyl)-3,4-dihydroquinazolin-1(2H)-yl)acetamido)methyl)phenyl)(imino)methyl)carbamate(86 mg, 0.1 mmol) was dissolved in CH₂Cl₂ (1 mL) and treated with TFA(600 P L). The resulting yellow solution was stirred for 3 h and thentreated with MeOH (150 μL), whereupon the solution immediately becamecolorless. The reaction mixture was evaporated to dryness and purifiedby chromatography (10% MeOH-CH₂Cl₂+1% 7 M NH₃-MeOH to yield benzyl((4-((2-(3-benzyl-7-carbamoyl-2,4-dioxo-3,4-dihydroquinazolin-1(2H)-yl)acetamido)methyl)phenyl)(imino)methyl)carbamateas a white solid (42 mg, 68% yield).

Step 7: Benzyl((4-((2-(3-benzyl-7-carbamoyl-2,4-dioxo-3,4-dihydroquinazolin-1(2H)-yl)acetamido)methyl)phenyl)(imino)methyl)carbamate(14 mg, 0.023 mmol) was dissolved in a mixture of MeOH (6 ml) and HOAc(3 mL). The resulting solution was degassed with a stream of nitrogenfor 2-3 min. 10% Pd/C (5 mg) was added, and the mixture was put undervacuum for approximately 1 minute. A balloon of hydrogen was applied,and the reaction was monitored for the consumption of starting material.The reaction mixture was filtered through a 0.2 m syringe filter andevaporated to dryness to give compound 2017 as a white solid (11 mg, 99%yield).

Example 303. Preparation of3-Benzyl-1-(2-((4-carbamimidoylbenzyl)amino)-2-oxoethyl)-N-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamide(2018)

Step 1: 3-Benzyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxylicacid (330 mg, 1.1 mmol) was suspended in CH₂Cl₂ (15 mL). To the stirredmixture was added methylamine (2 M in THF, 660 p L, 1.32 mmol) and DIEA(570 μL, 3.3 mmol). After 5 min at ambient temp, the reaction mixturebecame a clear solution. To this solution was added HATU (550 mg, 1.32mmol). Upon completion of reaction after 4 h, the reaction mixture waswashed with 1 M HCl, H₂O, and saturated aq NaHCO₃, then filtered througha glass fritted funnel to yield3-benzyl-N-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamideas a white solid (340 mg, quant).

Steps 2-5:3-Benzyl-1-(2-((4-carbamimidoylbenzyl)amino)-2-oxoethyl)-N-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamidewas prepared from3-benzyl-N-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamidefollowing similar protocols as described in steps 3-5, and 7 in Example4 (i.e., for compound 2017).

Example 304. Preparation of3-Benzyl-1-(2-((4-carbamimidoylbenzyl)amino)-2-oxoethyl)-N-cyclohexyl-2,4-dioxo-1,2,3,4-tetrahydoroquinazoline-7-carboxamide(2021)

Step 1: 3-Benzyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxylicacid (300 mg, 1.0 mmol) was suspended in CH₂Cl₂ (10 mL). To thisstirring mixture was added cyclohexylamine (140 μL, 1.2 mmol), DIEA (529μL, 3 mmol), HOBt (165 mg, 1.2 mmol) and EDC (234 mg, 1.2 mmol) insequential order. The mixture was stirred for 24 h. Upon completion, thereaction mixture was washed with 1 N HCl, and saturated aq NaHCO₃. Theorganic layer was dried over Na₂SO₄ and concentrated under vacuum toprovide3-benzyl-N-cyclohexyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamideas a white solid (200 mg, 52% yield).

Steps 2-5:3-Benzyl-1-(2-((4-carbamimidoylbenzyl)amino)-2-oxoethyl)-n-cyclohexyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamidewas prepared from3-benzyl-N-cyclohexyl-2,4-dioxo-1,2,3,4-tetrahydroquinazoline-7-carboxamidefollowing similar protocols to those described in steps 3-5, and 7 inExample 4 (i.e., for compound 2017).

Table 31 lists compounds of the Examples described above, as well asadditional compounds that may be prepared according to methods analogousto those described for the compounds above and other methods known to aperson having skill in the art.

TABLE 31 Compound List Exact Mass Exact Compound (ES+; M + H, Mass No.Structure Salt Obsd) (Calc) 1000

NA 304.20 303.17 1001

NA 318.15 317.19 1002

NA 330.20 329.19 1003

NA 330.12 329.19 1004

2HCl 339.26 338.24 1005

NA 346.13 345.22 1006

2HCl 353.28 352.26 1007

2HCl 356.00 355.20 1008

NA 358.20 357.22 1009

NA 362.16 361.18 1010

2HCl 363.28 362.24 1011

NA 366.12 365.19 1012

2HCl 368.26 367.20 1013

2HCl 368.25 367.24 1014

2HCl 369.25 368.22 1015

2HCl 370.16 369.22 1016

2HCl 370.17 369.22 1017

NA 372.23 371.23 1018

NA 372.23 371.23 1019

NA 372.18 371.23 1020

NA 373.16 372.22 1021

HCl 374.17 373.16 1022

NA 376.13 375.19 1023

NA 380.13 379.20 1024

2HCl 382.26 381.22 1025

2HCl 382.25 381.22 1026

NA 384.14 383.23 1027

2HCl 386.28 385.25 1028

NA 388.24 387.19 1029

NA 388.11 387.19 1030

NA 390.11 389.19 1031

HCl 390.17 389.15 1032

2HCl 392.22 391.20 1033

NA 392.10 391.20 1034

NA 392.12 391.20 1035

2HCl 394.25 393.22 1036

2HCl 394.23 393.22 1037

2HCl 394.23 393.22 1038

2HCl 394.22 393.48 1039

2HCl 393.12 (ES−) 394.21 1040

2HCl 395.12 394.21 1041

2HCl 396.13 395.23 1042

2HCl 396.27 395.23 1043

2HCl 396.28 395.23 1044

2HCl 396.15 395.23 1045

2HCl 396.18 395.23 1046

2HCl 396.17 395.23 1047

2HCl 400.24 399.21 1048

2HCl 400.24 399.21 1049

2HCl 400.14 399.21 1050

2HCl 400.24 399.21 1051

2HCl 400.30 399.26 1052

2HCl 402.20 401.19 1053

2 TFA 404.20 403.20 1054

2HCl 404.25 403.22 1055

NA 404.25 403.22 1056

2HCl 406.20 405.22 1057

2HCl 406.21 405.22 1058

NA 406.06 405.22 1059

2HCl 407.16 406.21 1060

2HCl 407.20 406.21 1061

2HCl 407.16 406.21 1062

2HCl 408.14 407.23 1063

2HCl 408.23 407.23 1064

2HCl 408.21 407.23 1065

2HCl 408.21 407.23 1066

2HCl 408.22 407.23 1067

2HCl 408.17 407.23 1068

2HCl 408.26 407.23 1069

NA 408.17 407.23 1070

2HCl 410.22 409.21 1071

2HCl 410.17 409.21 1072

2HCl 410.20 409.25 1073

2HCl 410.19 409.25 1074

2HCl 412.13 411.23 1075

2HCl 412.12 411.23 1076

2HCl 412.12 411.23 1077

NA 414.18 413.24 1078

HCl 416.16 415.17 1079

HCl 416.18 415.17 1080

2HCl 416.18 415.18 1081

2HCl 416.18 415.18 1082

2HCl 416.07 415.18 1083

NA 416.14 415.22 1084

2HCl 418.20 417.20 1085

2HCl 418.20 417.20 1086

2HCl 418.19 417.20 1087

2HCl 418.19 417.20 1088

2HCl 418.12 417.22 1089

2HCl 418.19 417.22 1090

2HCl 418.01 417.22 1091

2HCl 416.13 (ES−) 417.22 1092

2HCl 418.10 417.22 1093

2HCl 418.05 417.22 1094

2HCl 418.23 417.24 1095

2HCl 418.08 417.24 1096

NA 418.26 417.24 1097

2HCl 419.17 418.21 1098

2HCl 422.25 421.25 1099

2HCl 424.17 423.17 1100

NA 423.99 423.19 1101

2HCl 424.18 423.23 1102

NA 429.24 428.25 1103

2HCl 430.19 429.19 1104

2HCl 430.21 429.24 1105

NA 430.16 429.24 1106

2HCl 432.24 431.25 1107

NA 432.25 431.25 1108

2HCl 436.16 435.26 1109

NA 438.02 437.21 1110

2HCl 440.19 439.22 1111

2HCl 442.22 441.24 1112

2HCl 442.21 441.24 1113

NA 441.99 441.24 1114

NA 444.10 443.25 1115

NA 444.25 443.25 1116

NA 445.99 445.23 1117

NA 446.25 445.27 1118

2HCl 449.90 449.14 1119

2HCl 450.15 449.20 1120

2HCl 450.16 449.20 1121

NA 449.94 449.21 1122

2HCl 450.25 449.28 1123

2HCl 452.10 451.22 1124

2HCl 452.20 451.22 1125

2HCl 452.30 451.29 1126

2HCl 452.29 451.29 1127

NA 458.24 457.27 1128

2HCl 459.19 (ES−) 460.26 1129

NA 463.98 463.22 1130

2 HCl 464.32 463.29 1131

NA 466.09 465.24 1132

3HCl 467.30 466.31 1133

NA 468.07 467.24 1134

2HCl 472.25 471.26 1135

3HCl 473.15 472.26 1136

2HCl 474.19 473.20 1137

TFA 475.20 474.20 1138

NA 486.31 485.30 1139

2HCl 488.20 487.22 1140

2HCl 487.98 487.26 1141

2HCl 490.27 489.25 1142

2HCl 510.26 509.30 1143

2HCl 509.23 (ES−) 510.27 1144

3TFA 515.33 514.31 1145

2HCl 516.35 515.29 1146

NA 546.32 545.26 1147

2HCl 548.33 547.29 1148

3TFA 556.39 555.33 1149

2HCl 557.28 556.32 1150

2HCl 557.34 556.32 1151

2HCl 558.17 559.28 1152

2HCl 570.33 569.35 1153

2HCl 585.32 584.31 1154

NA 458.22 457.27 1156

NA 430.22 429.24 1157

2HCl 398.15 397.21 1158

2HCl 386.17 385.25 1170

1171

2HCl 421.14 420.23 1192

1HCl 408.12 407.12 1194

NA 316.11 315.17 1195

2HCl 404.17 403.22 1207

2HCl 380.25 379.20 1211

2HCl 557.34 536.32 1213

2HCl 384.27 383.23 1215

2HCl 386.15 385.21 1218

2HCl 388.28 387.26 1223

2HCl 509.22 510.27 1229

1HCl 476.18 475.19 999 (melagatran control)

429.24 1230

2 HCl 408.21 407.23 1231

2 HCl 422.25 421.25 1232

2TFA 570.38 569.35 1233

2TFA 540.33 539.28 1234

NA 440.18 439.2  1235

NA 422.2  421.19 1236

2TFA 532.34 531.28 1237

HCl 504.21 (ES−) 505.01 1238

TFA 420.2  419.2  1239

TFA 404.16 403.2  1240

NA 466.21 465.22 1241

HCl 422.26 421.25 1242

N/A 402.15 401.15 1243

2HCl 370.23 369.22 1244

2HCl 370.23 369.22 1245

2HCl 370.22 369.22 1246

HCl 419.13 418.14 1247

2HCl 408.22 407.23 1248

2 HCl 422.23 421.25 1249

2 HCl 422.24 421.25 1250

2TFA 634.31 633.31 1251

TFA 412.22 411.23 1252

2HCl 408.24 407.23 1253

HCl 396.27 395.23 1254

HCl 416.16 415.17 1255

2HCl 368.23 367.2 1256

2TFA 538.28 537.27 1257

2HCl 396.26 395.23 1258

NA 452.18 451.22 1259

NA 528.27 527.25 1260

NA 522.32 521.3  1261

2HCl 368.24 367.2  1262

2HCl 424.20 423.23 1263

NA 480.23 479.25 1264

NA 452.19 451.22 1265

N/A 382.25 381.22 1266

2HCl 386.22 385.21 1267

2HCl 374.24 373.19 1268

2TFA 515.27 514.27 1269

HCl 443.13 442.18 1270

2 HCl 383.25 382.21 1271

HCl 366.25 365.21 1272

2 HCl 395.22 394.21 1273

HCl 395.2  394.21 1274

HCl 479.12 478.14 1275

2HCl 390.17 389.16 1276

2HCl 462.16 461.20 1277

3HCl 423.20 422.24 1278

2HCl 419.19 418.21 1279

HCl 432.05 (ES−) 433.1 1280

2HCl 370.23 369.22 1281

2TFA 428.17 427.2  1282

2HCl 396.27 395.23 1283

2HCl 396.25 395.23 1284

2TFA 408.24 407.23 1285

2HCl 408.23 407.23 1286

HCl 408.14 407.14 1287

HCl 404.17 403.17 1288

NA 568.13 567.12 1289

HCl 396.24 395.23 1290

HCl 408.21 407.23 1291

2HCl 411.2  410.24 1292

NA 410.18 409.21 1293

NA 494.25 493.27 1294

NA 466.11 465.24 1295

NA 391.19 390.18 1296

2HCl 356.21 355.2  1297

2 HCl 446.1  445.25 1298

HCl 416.13 415.17 1299

HCl 404.15 403.17 1300

2TFA 412.19 411.21 1301

N/A 403.13 402.15 1302

2HCl 422.22 421.25 1303

2HCl 410.21 409.25 1304

2HCl 396.24 395.23 1305

NA 520.19 519.21 1306

2HCl 408.21 407.23 1307

HCl 430.12 429.18 1308

2 HCl 396.22 395.23 1309

2 HCl 447.13 446.24 1310

2HCl 398.19 397.21 1311

2HCl 392.2  391.2  1312

2TFA 516.24 515.29 1313

TFA 399.13 398.15 1314

TFA 379.11 (ES−) 380.18 1315

HCl 383.19 382.2  1316

2HCl 436.19 435.26 1317

HCl 481.06 480.19 1318

2HCl 464.12 463.22 1319

2HCl 504.24 503.29 1320

2TFA 478.09 477.2  1321

2TFA 478.14 477.2  1322

2HCl 410.2  409.25 1323

2HCl 396.2  395.23 1324

2TFA 446.16 445.25 1325

TFA 442.01 441.17 1326

2TFA 474.09 473.24 1327

2HCl 502.19 501.27 1328

2HCl 430.12 429.19 1329

2HCl 426.07 425.16 1330

2TFA 502.21 501.27 1331

2HCl 424.18 423.26 1332

2TFA 448.1  447.24 1333

HCl 400.12 399.17 1334

2HCl 440.04 439.18 1335

2TFA 439.15 438.24 1336

2HCl 357.16 356.2  1337

2HCl 410.15 409.25 1338

2HCl 446.1  445.25 1339

2TFA 520.17 519.24 1340

2HCl 486.21 485.28 1341

TFA 441.1  440.17 1342

2 HCl 446.07 445.25 1343

2TFA 447.12 446.24 1344

2HCl 410.17 409.25 1345

2HCl 543.23 542.3  1346

2HCl 356.18 355.2  1347

2 HCl 411.17 410.24 1348

2 HCl 425.18 424.26 1349

2HCl 489.27 490.14 1350

2HCl 474.02 473.14 1351

2HCl 472.12 471.26 1352

2TFA 570.21 569.26 1353

2 HCl 410.17 409.25 1354

2 HCl 410.24 409.25 1355

TFA 448.03 447.12 1356

TFA 516.16 515.21 1357

2TFA 473.13 472.26 1358

2TFA 402.1  401.16 1359

2TFA 458.04 457.25 1360

2TFA 458.12 457.25 1361

2TFA 479.10 478.22 1362

N/A 425.09 424.17 1363

HCl 444.08 443.2  1364

HCl 402.09 401.15 1365

HCl 430.1  429.18 1366

2HCl 392.2  391.2  1367

NA 393.19 392.2  1368

2HCl 531.26 530.3  1369

HCl 444.12 443.2  1370

TFA 480.13 479.2  1371

HCl 468.07 467.18 1372

2TFA 474.08 473.14 1373

2TFA 472.23 471.26 1374

HCl 508.08 507.09 1375

NA 494.18 493.22 1376

2TFA 427.16 426.24 1377

2TFA 440.21 439.29 1378

2TFA 494.21 493.22 1379

2TFA 450.14 449.28 1380

2 HCl 452.24 451.29 1381

2TFA 573.32 572.31 1382

2TFA 453.2  452.25 1383

TFA 396.24 395.22 1384

2HCl 427.12 426.16 1385

TFA 518.23 517.2  1386

TFA 411.16 410.15 1387

TFA 429.12 428.16 1388

NA 488.28 487.26 1389

2 HCl 407.21 406.21 1390

2TFA 408.19 407.2  1391

2TFA 479.29 478.27 1392

2TFA 490.19 489.19 1393

2TFA 516.25 515.21 1394

TFA 454.14 453.17 1395

TFA 436.16 435.11 1396

NA 515.29 514.25 1397

2TFA 533.24 532.26 1398

TFA 454.28 453.24 1399

2 HCl 478.29 477.22 1400

2 HCl 424.24 423.17 1401

HCl 506.27 505.21 1402

TFA 544.29 543.21 1403

NA 519.34 518.28 1404

HCl 545.29 544.21 1405

HCl 605.3  604.21 1406

2HCl 472.33 471.26 1407

2TFA 456.35 455.25 1408

HCl 546.2  545.13 1409

TFA 584.23 583.13 1410

TFA 512.27 511.18 1411

TFA 468.33 467.25 1412

TFA 510.38 509.3  1413

2TFA 424.36 423.26 1414

HCl 518.27 517.2  1415

HCl 490.26 489.19 1416

HCl 496.30 495.21 1417

TFA 426.23 425.16 1418

TFA 440.26 439.18 1419

TFA 528.28 527.2  1420

2TFA 479.36 478.27 1421

2TFA 465.19 464.12 1422

HCl 464.24 463.15 1423

HCl 464.32 463.24 1424

2TFA 532.29 531.21 1425

TFA 407.34 406.21 1426

TFA 468.26 467.18 1427

2TFA 486.35 485.28 1428

2TFA 421.35 420.23 1429

2TFA 421.35 420.23 1430

2TFA 488.38 487.26 1431

HCl 471.33 470.24 1432

HCl 480.30 479.21 1433

TFA 440.28 439.18 1434

2HCl 392.35 391.2  1435

2HCl 464.24 463.15 1436

TFA 526.3  525.15 1437

TFA 448.35 447.24 1438

2TFA 486.26 485.14 1439

TFA 482.39 481.27 1440

NA 510.43 509.3  1441

NA 410.36 409.25 1442

2HCl 440.3  439.18 1443

2HCl 464.26 463.15 1444

2HCl 464.28 463.15 1445

2HCl 476.18 475.12 1446

2HCl 398.37 397.21 1447

2TFA 414.46 413.22 1448

HCl 450.2  449.13 1449

2TFA 454.12 453.19 1450

2HCl 454.11 453.19 1451

2TFA 508.32 507.1  1452

2HCl 474.24 473.14 1453

HCl 476.20 475.26 1454

HCl 436.08 435.15 1455

2TFA 514.41 513.18 1456

HCl 470.01 469.1  1457

HCl 437.1  436.17 1458

2TFA 452.41 451.2  1459

2TFA 448.36 447.18 1460

2TFA 487.10 486.16 1461

HCl 436.08 435.15 1462

TFA 470.05 469.11 1463

2TFA 392.16 391.2  1464

NA 536.23 535.13 1465

2TFA 500.28 499.16 1466

2TFA 508.37 507.1  1467

TFA 392.19 391.2  1468

TFA 469.15 468.2  1469

HCl 411.21 410.24 1470

2TFA 438.16 437.22 1471

1TFA 409.1  408.16 1472

2TFA 406.18 405.22 1473

1TFA 520.48 519.2  1474

TFA 506.46 505.14 1475

2TFA 460.55 459.2  1476

HCl 468.16 467.21 1477

TFA 488.09 487.15 1478

HCl 476.18 475.26 1479

HCl 460.19 459.26 1480

2TFA 522.45 521.26 1481

2TFA 422.2  421.25 1482

HCl 532.05 531.1  1483

2TFA 513.97 513.06 1484

1TFA 564.28 563.15 1485

2 HCl 408.23 407.23 1486

2 HCl 408.21 407.23 1487

2HCl 408.22 407.23 1488* Purchased

NA 407.17 406.21 1489

NA 479.09 478.16 1490

AcOH 451.05 450.16 1491

TFA 443.17 442.21 1492

TFA 432.19 431.21 1493

2TFA 470.03 469.11 1494

2TFA 458.08 457.17 1495

2TFA 392.16 391.20 1496

NA 424.50 423.26 1497

2TFA 488.25 487.16 2000

2 HCl 227.11 226.10 2001

2 HCl 238.11 237.10 2002

2 HCl 252.07 251.12 2003

2 HCl 252.12 251.12 2004

2 HCl 252.11 251.12 2005

2 HCl 252.13 251.12 2006* Purchased

278.13 2007

2 HCl 266.11 265.13 2008

2 HCl 266.10 265.13 2009

2 HCl 277.09 276.11 2010

2 HCl 252.11 251.12 2011

2 HCl 282.13 281.13 2012

2 HCl 282.12 281.13 2013

2 HCl 288.13 287.12 2014

2 HCl 288.12 287.12 2015

2 HCl 291.07 290.13 2016

2 HCl 332.15 331.12 2017

HOAc 485.16 484.19 2018

HOAc 499.17 498.20 2019* Purchased

N/A N/A 422.20 2020* Purchased

N/A N/A 408.45 2021

N/A 567.15 566.26

Example 305. Enzymatic Assay for MASP-2

The MASP-2 assay utilizes a fluorogenic substrate, based on the cleavagesite for its natural substrate C2. The assay was run at room temperaturein an assay buffer containing 20 mM Hepes, pH 7.4, 140 mM NaCl and 0.1%Tween 20. Assay parameters were adjusted such that the assay was linearwith respect to time, enzyme and substrate concentrations. Under theseoptimized assays conditions, IC₅₀ values were equivalent to Ki values,except in a few cases of “tight binding” inhibitors. Cases of ‘tightbinding’ or possible ‘slow binding’ inhibitors were handled by themethods described in Copeland R. A. (2013) Evaluation of EnzymeInhibitors in Drug Discovery. 2nd Ed., John Wiley and Sons, Inc.,Chapters 5-7.

The MASP-2 assay protocol was carried out as follows. Test compoundswere serially diluted in DMSO and then 100 nL of each dilution wastransferred to the assay plate(s). 10 μL of Assay Buffer was added,followed by 15 μL of Enzyme (MASP-2 (CCP1-CCP2-SP) in Assay Buffer. 15μL of Substrate in Assay Buffer was then added and mixed to start thereactions. After 20 min at room temperature, 15 μL of a stop solution(0.1 M acetic acid) was added, mixed and the plates were read on aSpectraMax i3×Microplate Reader and exported as Excel files. Each assayplate included a “no inhibitor” (DMSO Only) control, a “no enzyme”control and a reference inhibitor control. % Activity values=100*(ave.test comp. fluorescence−ave. “no enz” fluorescence)/(ave. “DMSO only”fluorescence−ave.“no enz” fluorescence). IC₅₀ and Ki values were veryreproducible, falling well within ±2-fold.

Example 306. Lectin Pathway Activation Assay in Human Serum Treated withSmall Compounds

Microtiter ELISA plate was coated with mannan from Saccharomycescerevisiae (Sigma-Aldrich, M7504) for overnight at 4° C. in coatingbuffer [15 mM Na₂CO₃, 35 mM NaHCO₃]. Plate was blocked with 1% bovineserum albumin (BSA) (Sigma-Aldrich, A3294) in Tris-buffered Saline (TBS)[10 mM Tris-HCl, 140 mM NaCl] for 2 hours at room temperature. 1% humanserum was incubated with serial dilutions of small compounds in GVB++ [4mM Barbital, 145 mM NaCl, 0.2 mM MgCl₂, 0.2 mM CaCl₂, 1% Gelatin] andincubated for 15 minutes at room temperature. 100 μL of this mixturewere then added to the plate and plate was incubated at 37° C. for up toan hour with gentle shaking, 200 rpm. After that, plate was washedthrice in wash buffer [TBS containing 5 mM CaCl₂ and 0.05% Tween-20] and100 μL of rabbit anti human C3c (Dako, A0062) diluted 1:5000 in washbuffer were added and incubated at 37° C. for 30 minutes. Plate waswashed and 100 μL of HRP goat anti rabbit IgG (Southern Biotech,4050-05) diluted 1:8000 in wash buffer were added and incubated at roomtemperature for 30 minutes. After that, plate was washed three times and100 μL/well of TMB Colorimetric substrate (Thermo Scientific, 34029)were added and incubated at room temperature for 5 minutes and thereaction was stop by adding 100 μL/well of 0.1 N sulfuric acid (BDH7230)and the absorbance was measured at 450 nm.

Example 307. Enzymatic Assay for Thrombin

The thrombin assay utilizes a fluorogenic peptide substrate (Boc-VPR-AMC(R&D Systems) and was run at room temperature in an assay buffercontaining 20 mM Hepes, pH 7.4, 140 mM NaCl and 0.1% Tween 20. Assayparameters were adjusted such that the assay was linear with respect totime, enzyme and substrate concentrations. Under these optimized assaysconditions, IC₅₀ values were equivalent to Ki values, except in a fewcases of “tight binding” inhibitors. Cases of “tight binding” orpossible “slow binding” inhibitors were handled by the methods describedin Copeland R. A. (2013) Evaluation of Enzyme Inhibitors in DrugDiscovery. 2nd Ed. John Wiley and Sons, Inc., Chapters 5-7.

The thrombin assay protocol was carried out as follows. Test compoundswere serially diluted in DMSO and then 100 nl of each dilution wastransferred to the assay plate(s). 10 μL of Assay Buffer was added,followed by 15 μL of enzyme (human α-thrombin (BioPharm Lab.)) in assaybuffer. 15 μL of substrate in assay buffer were then added and mixed tostart the reactions. After 20 min at room temperature, 15 μL of a stopsolution (0.1 M acetic acid) was added, mixed and the plates were readon a SpectraMax i3×Microplate Reader and exported as Excel files. Eachassay plate included a “no inhibitor” (DMSO Only) control, a “no enzyme”control and a reference inhibitor control. % Activity values=100*(ave.test comp. fluorescence −ave.“no enz” fluorescence)/(ave. “DMSO only”fluorescence −ave.“no enz” fluorescence). IC₅₀ and Ki values were veryreproducible, falling well within ±2-fold.

The results of biological assays for the compounds listed in Table 31are listed in Tables 32, 33 and 34 below.

TABLE 32 MASP-2/Thrombin/Lectin Pathway Inhibition for Compounds1000-1229 MASP-2 mMASP-2 Thrombin Lectin Pathway MASP-2 vs. CompoundK_(i) (μM) K_(i) (μM) K_(i) (μM) IC₅₀ (μM) thrombin selectivity 1000 ***ND *** ND + 1001 ** ND *** ND −− 1002 ** ND **** ND ND 1003 *** ND ****ND −− 1004 *** ND **** ND −− 1005 ** ND **** ND −− 1006 **** **** ****ND −− 1007 **** ** * ND *** 1008 *** ND **** + −− 1009 ** ND *** ND −−1010 **** ND −− ND **** 1011 **** ND **** ++ −− 1012 *** ND −− ND ***1013 ** ND * ND ** 1014 ** ND −− ND ** 1015 *** * −− + * 1016 *** * −− +** 1017 **** ND **** ND −− 1018 ** ND **/*** −− −− 1019 *** ND *** ND −−1020 **** ND **** ND −− 1021 ** −− −− −− *** 1022 * ND *** ND −− 1023*** ND **** + −− 1024 **** ND **** +++/++++ ** 1025 **** ND −− ++ ****1026 *** ND **** ND ** 1027 **** ND **** ++/+++ −− 1028 ** ND **** ND −−1029 ** ND *** ND −− 1030 **** **** ** ++ *** 1031 *** ND * ND ** 1032**** ND ** ND **** 1033 ** ND ** ND −− 1034 **** ND *** +/++ * 1035 ****ND **** ++++ ** 1036 **** **** ***/** +++/++++ **** 1037 **** ND *** ND*** 1038 **** ND **** +++/++++ * 1039 ** * −− ND *** 1040 **** **** −−++ **** 1041 *** ND **** + −− 1042 **** ND **** ++++ ** 1043 **** ******* ++/+++ ** 1044 **** **** **** ND ** 1045 **** **** **** ND ** 1046**** **** **** ND ** 1047 **** **** **** ++/+++ ** 1048 **** **** ****++/+++ ** 1049 **** ND **** ND ** 1050 **** ND ** ND ND 1051 ** ND**** + −− 1053 **** ND ** ++ ** 1054 *** ND ** + * 1055 *** ND **** + −−1056 **** ND *** ND **** 1057 **** ND *** ND **** 1058 **** ND ****++/+++ −− 1059 **** **** −− ++/+++ **** 1060 ****/*** −− −− −− *** 1061**** ND *** ND * 1062 *** ND * ND *** 1063 **** ND *** ND ** 1064 *** ND** ND ** 1065 **** **** * ++++ **** 1066 **** ND −− ND *** 1067 ******** ** ND **** 1068 *** ND * ND ** 1069 **** ND **** ++ −− 1070 ** ND−− ND * 1071 **** **** ** ND *** 1072 **** **** **** ND ** 1073 ******** **** ND ** 1074 **** **** **** ND ** 1075 **** **** **** ND ** 1076**** ND **** ND ** 1077 ** ND **** ND −− 1078 **** ND ND ++ ND 1079 ****ND ND + ND 1080 **** **** **** ++/+++ ** 1081 **** **** **** ++/+++ **1082 **** ND **** ND * 1083 **** ND **** + −− 1084 **** ND **** ND **1085 **** ND **** ND ** 1086 **** ND **** ND ** 1087 **** ND **** ND **1088 **** **** *** +++ ** 1089 **** ND ** ND *** 1090 **** **** **/* ++*** 1091 *** **** −− + *** 1092 **** **** **** ++/+++ −− 1093 **** ND**** ND −− 1094 **** ND **** + −− 1095 ** ND ** ND * 1096 *** ND ****+/++ −− 1097 **** **** **** ND *** 1098 **** ND ND ++++ ND 1099 **** ND**** +++ −− 1100 *** ND **** ND −− 1101 **** **** *** ND * 1102 *** ND**** ND −− 1103 **** **** **** +++ ** 1104 * ND *** ND −− 1105 ** ND ***ND −− 1106 *** ND **** ND −− 1107 **** ND **** ++/+ −− 1108 **** ******** ND * 1109 ** ND **** −− −− 1110 **** ND **** +++/++++ * 1111 ****ND **** ND * 1112 **** ND **** ND ** 1113 ** ND *** ND −− 1114 **** ND**** ++ −− 1115 **** ND **** ++ −− 1116 *** ND **** + −− 1117 ** ND ****ND −− 1118 **** **** **** ND ** 1119 **** ND *** ND ** 1120 **** ND ****ND ** 1121 ** ND *** ND −− 1122 **** ND **** ND −− 1123 **** ND *** ++** 1124 **** ND **** +++/++++ −− 1125 **** **** **** ND −− 1126 **** ND**** ND −− 1127 *** ND **** + −− 1128 **** **** **** ND * 1129 **** ND**** ++ −− 1130 **** ND **** ND −− 1131 **** ND **** ++ −− 1132 *** NDND ND ND 1133 **** ND **** + −− 1134 **** **** **** ND −− 1135 **** ND*** ND * 1136 **** ND *** ND *** 1137 *** ND ND −− ND 1138 ** ND **** ND−− 1139 **** ** *** + * 1140 **** ND **** ND −− 1141 **** ND **** ND −−1142 **** ND **** ND * 1143 **** **** **** ND −− 1144 *** ND ND ND ND1145 **** ND ND +++ ND 1146 **** ND *** ND * 1147 *** ND *** ND * 1148**** ND ND ND ND 1149 **** **** **** ND ** 1151 **** ND **** ND −− 1152**** ND **** ND * 1153 **** ND **** ND **** 1154 **** ND **** ND −−1156 * ND ***/**** ND −− 1157 * ND −− ND * 1158 * ND **** ND −− 1170**** * −− ND **** 1171 * * −− −− * 1192 * ND −− ND * 1194 * ND ** ND −−1195 * ND * ND −− 1207 ** ND *** ND −− 1211 **** ND **** ND −− 1213 * ND−− ND * 1215 ** * −− ND * 1218 **** ND **** ND −− 1223 **** **** **** ND*** 1229 ** ND ** ND * 999 **** **** **** +/++ −− (melagatran control)MASP-2 Inhibition and Thrombin Inhibition Ki Values: * K_(i) of lessthan 25 μM ** K_(i) of less than 10 μM *** K_(i) of less than 2.5 μM**** K_(i) of less than 0.5 μM −− K_(i) of >25 μM Lectin PathwayInhibition −− IC₅₀ value >50 μM + IC₅₀ value in the range of 5 μM to 50μM ++ IC₅₀ value in the range of 0.5 μM to 5 μM +++ IC₅₀ value in therange of 0.05 μM to 0.5 μM ++++ IC₅₀ value <0.05 μM Selectivity ofcompound for MASP-2 inhibition versus thrombin: −− less than 1.0-fold *1.0 to 5.0-fold ** 5.0 to 25-fold *** 25 to 100-fold **** >100-fold NDNot determined

TABLE 33 MASP-2/Thrombin/Lectin Pathway Inhibition for Compounds1230-1497 MASP-2 K_(i) mMASP-2 Thrombin Lectin Pathway MASP-2 vs.thrombin Compound (μM) K_(i) (μM) K_(i) (μM) IC₅₀ (μM) selectivity 1230**** **** * ++++ **** 1231 **** **** ** ND **** 1232 *** ND **** ND −−1233 **** **** *** ND * 1234 **** **** * ND *** 1235 **** ND * ND ***1236 **** **** **** ND * 1237 * ND *** ND −− 1238(:02 **** **** ** ND*** 1239 **** **** ** ++ ** 1240 *** ND * ++ ** 1241 **** **** **** ND *1242 *** ** ** ND ** 1243 * ND −− ND ND 1244 *** ND −− ND ** 1245**** * * ND **** 1246 * ND * ND * 1247 **** **** *** ND *** 1248 ******** *** ND ** 1249 **** **** * ND **** 1250 **** **** **** ND * 1251*** ND **** ND −− 1252 **** ND ** ND *** 1253 **** *** −− +++ ND 1254**** ND * ND *** 1255 *** ND −− ND ND 1256 **** ND **** ND * 1257 **** *−− ND *** 1258 ** ND −− ND ND 1259 ** ND −− ND ND 1260 ** ND −− ND ND1261 * * −− ND * 1262 **** ND *** ND *** 1263 ** ** −− ND ND 1264 ** *−− ND ND 1265 **** ** −− ND **** 1266 *** −− −− ND ** 1267 ** −− −− NDND 1268 **** **** **** ND * 1269 *** * −− ND ** 1270 **** **** **** ND** 1271 ** −− −− ND ND 1272 **** **** *** ND *** 1273 * * −− ND ND 1274** * −− ND ** 1275 *** −− −− ND *** 1276 **** **** *** ND *** 1277 ******** **** ND ** 1278 **** **** ** ND *** 1279 *** −− ** ND ** 1280 ** *−− ND ND 1281 ** −− −− ND ND 1282 * −− −− ND ND 1283 **** *** ** ND ***1284 **** **** **** ND * 1285 *** *** ** ND ** 1286 ** **** *** ND −−1287 * −− −− ND ND 1288 ** ** −− ND ND 1289 **** **** **** ND −− 1290**** **** *** ND ** 1291 *** * −− ND ND 1292 ** * −− ND ND 1293 ** ** −−ND * 1294 ** ** −− ND ND 1295 **** **** ** ND *** 1296 ** −− −− ND **1297 **** **** * ND **** 1298 **** ** −− ND ND 1299 **** * −− ND ****1300 **** **** ** ND *** 1301 ** −− −− ND ND 1302 **** **** *** ND ***1303 **** ** −− ND *** 1304 **** *** *** +++ *** 1305 *** **** −− ND **1306 **** **** **** ND * 1307 **** **** −− +++ **** 1308 *** *** * ND **1309 **** **** −− ND **** 1310 *** −− −− ND *** 1311 ** ** −− ND * 1312**** **** **** ND * 1313 ** −− * ND * 1314 * −− −− ND * 1315 *** **** **ND * 1316 **** **** *** ND *** 1317 **** *** −− ND ND 1318 **** **** **ND **** 1319 **** * ** ND ** 1320 **** *** *** ND ** 1321 * −− −− ND ND1322 **** *** * ND *** 1323 −− * −− ND ND 1324 **** **** *** +++ ***1325 *** * **** ND −− 1326 **** **** * ND *** 1327 **** **** **** ND ***1328 **** **** *** +++ **** 1329 **** **** *** ND * 1330 **** **** ****ND *** 1331 **** **** −− +++ **** 1332 * ** −− ND ND 1333 ** * −− ND ND1334 **** **** **** +++ −− 1335 **** **** ** ND *** 1336 * −− −− ND ND1337 **** **** *** ++ **** 1338 **** **** −− +++ **** 1339 **** ******** ++++ ** 1340 **** **** **** ND ** 1341 * −− *** ND −− 1342 ******* * ND **** 1343 **** **** ** +++ **** 1344 **** **** ** ND **** 1345**** **** **** ++++ **** 1346 * −− −− ND ND 1347 **** **** *** ++++ ***1348 **** **** **** ++++ *** 1349 *** ** −− ND ** 1350 **** **** ** ++**** 1351 **** **** −− ++++ **** 1352 **** **** *** +++ *** 1353 ******** **** ++++ *** 1354 **** *** ** ND *** 1355 **** * −− ND ND 1356**** **** −− +++ **** 1357 **** **** −− ++++ **** 1358 *** −− −− ND ND1359 *** * −− ND ** 1360 **** **** −− +++ **** 1361 **** **** −− ++++**** 1362 *** *** *** ND * 1363 **** **** ** +++ **** 1364 *** * −− NDND 1365 **** **** −− ++++ **** 1366 ** ** −− ND ND 1367 **** * −− ND ND1368 *** * −− +++ ** 1369 **** **** −− ND **** 1370 **** *** −− +++ ND1371 **** *** **** +++ −− 1372 **** **** **** +++ ** 1373 **** **** ***+++ *** 1374 **** **** −− ND ND 1375 *** * * ++ ** 1376 *** −− −− ND ND1377 *** −− * +++ ** 1378 **** **** *** ++ * 1379 **** **** −− ++ ****1380 *** **** −− −− *** 1381 *** * * ++ ** 1382 **** ** −− + *** 1383*** ** −− + ND 1384 * −− −− ND * 1385 **** **** **** +++ ** 1386 * −− −−ND ND 1387 ** * −− ND ND 1388 **** **** −− ++++ **** 1389 **** ** −− ++**** 1390 ** −− −− ND ND 1391 **** **** −− ++ **** 1392 **** **** *** ++*** 1393 **** **** **** +++ * 1394 ** −− * ND * 1395 *** ** −− + ND 1396**** **** −− ++ **** 1397 **** **** −− +++ **** 1398 **** *** −− +++ ND1399 **** **** * +++ **** 1400 **** ** −− ++ ND 1401 **** *** −− ND ND1402 **** *** **** ND * 1403 **** *** −− ND ND 1404 **** **** **** ND **1405 **** *** *** ND ** 1406 **** **** ** +++ **** 1407 **** **** ** +++**** 1408 **** ** ** ND ** 1409 **** ** **** ++ * 1410 **** *** *** ++*** 1411 **** **** −− +++ ND 1412 **** ** −− ND ND 1413 *** ** −− ND ***1414 **** **** **** +++ −− 1415 **** **** **** +++ * 1416 **** **** ****+++ ** 1417 *** ** −− ND ND 1418 ** * −− ND ND 1419 **** **** ****++++ * 1420 **** **** ** +++ **** 1421 **** *** * ND **** 1422 **** ****** ++ **** 1423 **** **** ** +++ **** 1424 *** *** **** ND ND 1425 ***** −− ND ND 1426 **** *** *** ++++ *** 1427 **** **** −− ND **** 1428**** *** * ++ **** 1429 **** **** ** ++ **** 1430 **** **** −− ++ ****1431 **** **** * +++ **** 1432 **** **** * ++ **** 1433 **** **** ***+++ **** 1434 * * −− ND ND 1435 **** **** * ++ **** 1436 *** −− * ND **1437 *** ** −− ND ** 1438 **** *** **** ++ ** 1439 **** ** −− ND ND 1440**** ** −− ND ND 1441 **** **** −− +++ ND 1442 **** **** −− ++ ND 1443**** **** *** ++ *** 1444 **** **** **** ++ ** 1445 **** *** −− + ****1446 **** *** −− + **** 1447 **** **** ** ++ **** 1448 **** ** −− ND**** 1449 **** **** ** ++ **** 1450 **** **** ** +++ **** 1451 ******** * ++ **** 1452 **** **** *** ++ **** 1453 **** **** * ++++ ****1454 **** **** *** ++ *** 1455 **** **** −− ND **** 1456 **** *** −− +ND 1457 * ** −− ND ND 1458 **** **** −− ND **** 1459 **** **** ** ND**** 1460 **** **** −− ND **** 1461 **** **** *** ND **** 1462 *** ** *ND ** 1463 **** **** −− ND ND 1464 **** **** −− ND ND 1465 **** *** ****ND * 1466 **** **** * ND **** 1467 **** *** −− ND **** 1468 **** **** −−ND **** 1469 **** **** ** ND **** 1470 **** **** ** ND **** 1471 ** **−− ND ND 1472 **** **** ** ND **** 1473 **** **** −− ND ND 1474 ******** −− ND **** 1475 **** **** * ND **** 1476 **** **** ** ND **** 1477**** **** * ND **** 1478 **** **** * ND **** 1479 **** **** * ND ****1480 **** *** −− ND **** 1481 **** **** ** ND **** 1482 **** **** *** ND*** 1483 **** **** * ND **** 1484 *** *** −− ND ND 1485 **** **** *** ND** 1486 *** **** ** ND ** 1487 **** ND −− ND *** 1488*Purchased **** ****** ++ −− 1489 **** *** **** ND −− 1490 **** ** **** + −− 1491 *** ******** + −− 1492 **** **** **** +++ ** 1493 * −− * ND * 1494 **** **** **ND **** 1495 ** *** −− ND ** 1496 **** *** −− ND ND 1497 **** ** ** ND** MASP-2 Inhibition and Thrombin Inhibition Ki Values: * 10 μM < K_(i)≤ 25 μM ** 2.5 μM ≤ K_(i) < 10 μM *** 0.5 μM ≤ K_(i) < 2.5 μM **** K_(i)<0.5 μM −− K_(i) of >25 μM ND Not determined Lectin Pathway Inhibition +5 μM < IC₅₀ ≤ 50 μM ++ 0.5 μM ≤ IC₅₀ < 5 μM +++ 0.05 μM ≤ K_(i) < 0.5 μM++++ K_(i) <0.05 μM −− IC₅₀ >50 μM Selectivity of compound for MASP-2inhibition versus thrombin: −− <1.0-fold * ≥1.0 to <5.0-fold ** ≥5.0 to<25-fold *** ≥25 to <100-fold **** ≥100-fold ND Not determined

TABLE 34 MASP-2/Thrombin/Lectin Pathway Inhibition MASP-2 versusCompound MASP-2 K_(i) Thrombin K_(i) Lectin thrombin No. (μM) (μM) K_(i)selectivity 2000 **** (+Zn) ** (+Zn) ND ++ (+Zn) −− (+EDTA) −− (+EDTA)2001 **** (+Zn) *** (+Zn) ND ++ (+Zn) −− (+EDTA) −− (+EDTA) 2002 ***(+Zn) * (+Zn) ND ++ (+Zn) −− (+EDTA) −− (+EDTA) 2003 ***** (+Zn) ***(+Zn) ND +++ (+Zn) −− (+EDTA) −− (+EDTA) 2004 **** (+Zn) **** (+Zn) ND +(+Zn) −− (+EDTA) −− (+EDTA) 2005 ***** (+Zn) ***** (+Zn) ND + (+Zn) −−(+EDTA) −− (+EDTA) 2006 ** (+Zn) −− (+Zn) ND + (+Zn) −− (+EDTA) −−(+EDTA) 2007 **** (+Zn) *** (+Zn) ND ++ (+Zn) −− (+EDTA) −− (+EDTA) 2008**** (+Zn) ** (+Zn) ND +++ (+Zn) −− (+EDTA) −− (+EDTA) 2009 **** (+Zn)*** (+Zn) ND ++ (+Zn) −− (+EDTA) * (+EDTA) 2010 ***** (+Zn) *** (+Zn) ND++ (+Zn) −− (+EDTA) * (+EDTA) 2011 **** (+Zn) *** (+Zn) ND ++ (+Zn) −−(+EDTA) −− (+EDTA) 2012 ***** (+Zn) **** (+Zn) ND + (+Zn) −− (+EDTA) −−(+EDTA) 2013 **** (+Zn) ** (+Zn) ND ++++ (+Zn) −− (+EDTA) −− (+EDTA)2014 **** (+Zn) *** (+Zn) ND +++ (+Zn) −− (+EDTA) * (+EDTA) 2015 ***(−Zn) *** (−Zn) ND + (+Zn) ***** (+Zn) **** (+Zn) −− (+EDTA)] −−(+EDTA)] 2016 **** (+Zn) * (+Zn) ND +++ (+Zn) −− (+EDTA) * (+EDTA) 2017*** −− ND >++ 2018 *** −− ND >++ 2019 ** −− ND >+ 2020 * −− ND >+ 2021** −− + >++ MASP-2 Inhibition and Thrombin Inhibition Ki values: * K_(i)of less than 25 μM ** K_(i) of less than 10 μM *** K_(i) of less than2.5 μM **** K_(i) of less than 0.5 μM ***** K_(i) of less than 0.05 μM−− K_(i) of >25 μM Lectin Pathway Inhibition: −− IC₅₀ value >50 μM +IC₅₀ value in the range of 5 μM to 50 μM Selectivity of compound forMASP-2 versus thrombin: −− less than 1.0-fold + 1.0 to 5.0-fold ++ 5.0to 25-fold +++ 25 to 100-fold ++++ >100-fold ND Not determined

Example 308. MASP-2 Protein Preparation

This example illustrates the preparation of recombinant MASP-2 protein,based on UniProt O00187, human mannan-binding lectin serine protease 2.Expression constructs for human MASP-2 CCP2-SP and CCP2-SP-6HIS weregenerated for recombinant expression in E. coli cells.

Recombinant expression of MASP-2 in E. coli as inclusion bodies andprotein purification was carried out according to methods described inAmbrus G. et al., 2003, with minor modifications. For the HIS taggedversion, the MASP-2 protein (CCP2-SP-6HIS) was purified under denaturingconditions according to the methods described in Ni-NTA SuperflowCartridge Handbook, Qiagen, March 2007.

Purification of MASP-2 included extraction, unfolding, refolding andchromatography using standard methods as described by Harmat et al., J.Mol. Biol. 2004; 342:1533-1546; and Gal et al., J. Biol. Chem. 2005;280:33435-33444; and Ambrus et al. J Immunol. 2003 Feb. 1;170(3):1374-82. After size exclusion chromatography, the recombinantMASP-2 protein was concentrated from 5 mg/mL to 20 mg/mL with spinconcentrator (Amicon NMWL 10 kDa). Concentrated MASP-2 protein sampleswere flash-frozen and stored until thawing for complex formation.Purification and cleavage were monitored by SDS-PAGE stained byCommassie Blue Simply Blue™ Safe Stain (Invitrogen).

Example 309. MASP-2 Co-Crystallization

To prepare co-crystallization solutions of MASP-2 with inhibitorycompounds, the compounds were dissolved in aqueous solution at aconcentration of 100 mM to 10 mM. Such stock solutions were diluted 1:10into MASP-2 protein samples at a protein concentration of 5 to 20 mg/mL.

Crystallization trials were setup as sitting drop, vapor diffusionexperiments by combining equal volumes of MASP-2 compound complexsolution with commercially available crystallization formulations.Typically, crystallization hits were obtained by screening against two96-well crystallization reagent kits (GRAS6, GRAS2, Hampton Research;MORPHEUS, Molecular Dimensions; Wizard 1&2 Cryo, Rigaku Reagents) andcrystal growth was inspected by optical microscopy. Crystals were useddirectly or further optimized for X-ray diffraction. Crystals werecaptured with cryogenic loops and dipped into liquid nitrogen directlyor cryoprotected with a 20% glycerol in crystallization formulationbefore flash-cooling in liquid nitrogen.

Listing of compound-MASP-2 crystallographic structures with theirrespective construct employed, as well as resulting space group anddimensions are provided for each co-crystal structure in Table A3(Appendix).

In cases where multiple ligand poses within a single or multiplecrystallographic units were observed, and in cases where crystalstructures of multiple space groups were obtained, the mostrepresentative pose was selected for hydrogen bonding and van der Waalscontacts analysis.

Example 310. MASP-2 Crystal Soaking

To prepare crystals that contain complexes of MASP-2 bound withinhibitory compounds, crystals grown with weakly bound compounds can bewashed and soaked. At first MASP-2 compound complex crystals are grown,for instance with compound 43 and individual crystals are washed twice,for a minimum of 4 h with the crystallization solution lacking anyinhibitor compounds. Thereafter crystals are transferred once or twicefor soaking within the crystallization solution containing the MASP-2inhibitor. Further crystal handling and data processing is carried outas described in the immediately preceding Example 307.

Example 311. X-ray Crystallography X-Ray Diffraction and StructureDetermination

Crystals were diffracted with synchrotron X-rays of 1.0 wavelength andX-ray diffraction datasets were collected at beamlines SSRL BL9-2,BL14-1, BL12-2 as well as ALS sector 5 using Dectris Pilatus and Eigerdetectors. Structures were determined by molecular replacement usingportions of the structure 1Q3X as search models and partially refinedwith Buster 2.10.2 or Refmac 5.8. Electron densities were inspected withCoot (Emsley et al., 2010) and subjected to iterative refinement cyclesuntil the density of ligand in the binding pocket was clearly visibleand R-factors sufficient; at this point the partial refinement wasdeemed completed and models for ligand, solvent and protein wereinspected. When multiple ligand poses were observed, for instancearising from multiple molecules in the asymmetric unit or refined dualposes within the same molecule, only one pose was selected and analyzed.

Example 312. Structure Analysis

Partially refined structures were analyzed for ligand-protein and-solvent interaction types and distances, using LigPlot+(Laskowski andSwindells, 2011) and ICM-Pro (Molsoft, LLC) software with parameters setfor 3.35 Å for the maximum distance between hydrogen bond donor andacceptor; and non-bonded contact parameters between hydrophobic to anycontacts, such as van der Waals interactions with maximum contactdistance of 3.90 Å. Table A2 (Appendix) shows van der Waals interactionsof MASP-2 atoms with compound atoms that result by LigPlot-basedanalysis of the crystallographic structures. LigPlot+ calls these‘nonbonded contacts’ or ‘hydrophobic contacts’. Despite the name, thereare atom pairings that include possible H-bonds. Thus, in someinstances, the Table A2 also contains H-bond interactions.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1129)through van der Waals interactions. van der Waals interactions includeweak, short-range electrostatic attractive forces between unchargedmolecules, arising from the interaction of permanent or transientelectric dipole moments.

As shown in Table A2, 1129 Compound atom CO2 interacts with atom CD2 inHIS483. C30 interacts with CE1 of PHE 529, and atoms N04, CO3 and CO1interact with CZ of PHE529. PRO 606 carbon atom C of MASP-2 CCP2-SPamino acid interacts with (1129) through C28. In addition, amidinenitrogen N19 interacts with carbon CG of ASP 627. Carbon C14 of (1129)interacts with C of SER 628. Carbons C18, C15 and C14 of (1129)interacts with an oxygen on SER 628. C14 of (1129) also interacts withoxygen OG on SER 628. C17 and C12 of (1129) interacts with carbon CA ofCYS 629. Carbons C13, C12 and C11 of (1129) interacts with oxygen O ofCYS 629. Oxygen O25 of (1129) interacts with carbon CD and CG of ARG630. Oxygen O8 interacts with carbon CG of ARG 630. Carbon C17 interactswith the nitrogen of ARG 630. Carbon C11 and carbon 06 interact withoxygen OG of SER 633. Carbon C13 interacts with carbon CG1 of VAL 653.Nitrogen N10 interacts with carbon C of SER 654. Carbon C11, C06 and C01 interact with carbon C of SER 654. Carbons C14 and C13 and oxygen O07interact with carbon C of TRP 655. Nitrogen N10 and oxygen O07 interactwith carbon CA of TRP 655. Oxygen O7 interacts with carbon CB of TRP655. Carbons C14 and C13 interact with oxygen O of TRP 655. Nitrogen N20of (1129) interacts with carbon C of GLY 656. Nitrogen N20 and carbonsC18 and C15 all interact with carbon CA of GLY 656. Carbons C16 and 15interact with nitrogen N of GLY 656. Carbons C23, C09 and C05 interactwith oxygen O of GLY 656. Carbon C23 and nitrogen N20 interact withcarbon C of SER 657. Carbons C24, C23 and C16 interact with oxygen O ofSER 657. Oxygen O25 and carbon C24 interact with carbon CA of MET 658.Oxygen O26 interacts with carbon CG of MET 658. Nitrogen N19 interactswith carbons CA and CB of CYS 660. Carbon C18 interacts with carbon CBof CYS 660. Nitrogen N20 and carbons C18, C16 and C15 interact withsulfur SG of CYS 660. Carbon C18 interacts with oxygen OE1 of GLN 665.Nitrogen N19 interacts with carbon CA of GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1034)through van der Waals interactions. As shown in Table A2, carbon C28 of(1034) interacts with carbon CG of PRO 606. Nitrogen atom O4, CO3, CO2and CO1 of (1034) interact with CZ of PHE 529. Carbons C28 and C27interact with oxygen O of PRO 606. Nitrogen N20 interacts with carbon CGof ASP 627. Carbon C16 interacts with carbon C of SER 628. Carbons C18,C16 and C15 interact with oxygen O of SER 628. Carbon C16 of (1034)interacts with oxygen OG of SER 628. Carbons C17, C13, C12, C11, C17,C14, C13 and C12 interact with carbon CA of CYS 629. Carbon C12 and C11interact with oxygen O of CYS 629. Carbon C11 of (1034) interacts withcarbon CA of ARG 630. Carbons C13, C12, C11 interact with nitrogen N ofARG 630. Carbon C11 interacts with oxygen OG of SER 633. Carbon C11 of(1034) interacts with carbon C of SER 654. Carbons C17 and C16 andoxygen O07 interact with carbon C of TRP 655. Oxygen O07 interact withcarbon CA of TRP 655. Oxygen O7 and carbon 05 interacts with carbon CBof TRP 655. Carbon C16 interacts with oxygen O of TRP 655. Nitrogen N19and oxygen O7 of (1129) interacts with carbon C of GLY 656. Nitrogen N19and carbon C18 and oxygen O07 all interact with carbon CA of GLY 656.Carbons C24, C09 and C05 interact with oxygen O of GLY 656. Nitrogen N19interacts with carbon C of SER 657. Nitrogen N19 interacts with carbonCA of SER 657. Carbons C18, C14 interact with oxygen O of SER 657.Nitrogen N19 interacts with carbon CD of GLN 665. Carbon C18 interactswith oxygen OE1 of GLN 665. Nitrogen N20 interacts with carbon CA of GLY667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1024)through van der Waals interactions. As shown in Table A2, specific atomsof (1024) interact with specific atoms of TYR 607, PRO 608, SER 611, ASP627, SER 628, CYS 629, ARG 630, SER 633, SER 654, TRP 655, GLY 656, SER657, and GLY 667 in a manner similar to the entries 1 and 2 of Table 9and above.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1059)through van der Waals interactions. As shown in Table A2, specific atomsof (1059) interact with specific atoms of TYR 607, PRO 608, ASP 627, SER628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER657, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1088)through van der Waals interactions. As shown in Table A2, specific atomsof (1088) interact with specific atoms of PRO 606, TYR 607, PRO 608, ASP627, SER 628, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER657, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1036)through van der Waals interactions. As shown in Table A2, specific atomsof (1088) interact with specific atoms of ASP 627, SER 628, CYS 629, ARG630, SER 633, SER 654, TRP 655, GLY 656, SER 657, ASN 659, CYS 660, andGLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1081)through van der Waals interactions. As shown in Table A2, specific atomsof (1081) interact with specific atoms of SER 611, ASP 627, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER 657, andGLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1063)through van der Waals interactions. As shown in Table A2, specific atomsof (1063) interact with specific atoms of SER 611, ASP 627, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER 657, andGLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1065)through van der Waals interactions. As shown in Table A2, specific atomsof (1065) interact with specific atoms of TYR 607, PRO 608, SER 611, ASP627, SER 628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1030)through van der Waals interactions. As shown in Table A2, specific atomsof (1030) interact with specific atoms of ASP 627, SER 628, ARG 630, SER633, SER 654, TRP 655, GLY 656, SER 657, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1037)through van der Waals interactions. As shown in Table A2, specific atomsof (1037) interact with specific atoms of PRO 606, ASP 627, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER 657, MET658, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1118)through van der Waals interactions. As shown in Table A2, specific atomsof (1118) interact with specific atoms of TYR 607, PRO 608, SER 611, ASP627, SER 628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1007)through van der Waals interactions. As shown in Table A2, specific atomsof (1007) interact with specific atoms of TYR 607, SER 611, ASP 627, SER628, CYS 629, ARG 630, SER 633, SER 654, TRP 655, GLY 656, SER 656, andMET 658.

In certain aspects, MASP-2 CCP2-SP amino acids interact with(melagatran) through van der Waals interactions. As shown in Table A2,specific atoms of (melagatran) interact with specific atoms of TYR 607,ASP 627, SER 628, CYS 629, ARG 630, SER 633, SER 654, TRP 655, GLY 656,SER 657, MET 658, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1090)through van der Waals interactions. As shown in Table A2, specific atomsof (1090) interact with specific atoms of PRO 606, TYR 607, PRO 608, ASP627, SER 628, CYS 629, ARG 630, SER 633, TRP 655, GLY 656, and SER 657.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1089)through van der Waals interactions. As shown in Table A2, specific atomsof (1089) interact with specific atoms of PRO 606, ASP 627, SER 628, ARG630, SER 633, SER 654, TRP 655, GLY 656, SER 657, CYS 660, and GLY 667.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1021)through van der Waals interactions. As shown in Table A2, specific atomsof (1021) interact with specific atoms of ASP 627, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY 656, SER 657, MET 658, GLY667 and TYR 669.

In certain aspects, MASP-2 CCP2-SP amino acids interact with (1097)through van der Waals interactions. As shown in Table A2, specific atomsof (1118) interact with specific atoms of PRO 606, TYR 607, PRO 608, ASP627, SER 628, CYS 629, ARG 630, SER 633, SER 654, TRP 655, GLY 656, SER657, MET 658, CYS 660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (54) through van der Waals interactions. As shown in TableA2, specific atoms of compound (54) interact with specific atoms of ALA468, ALA 469, PHE 529, SER 628, CYS 629, ARG 630, GLY 631, ASP 632, GLY634, GLY 635, VAL 653, SER 654, TRP 655, GLY656, SER 657, and MET 658.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (54) through van der Waals interactions. As shown in TableA2, specific atoms of compound (54) interact with specific atoms of GLY528, ASP627, SER628, CYS 629, ARG 630, SER 633, VAL653, SER 654, TRP655, GLY 656, SER 657, CYS 660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (54) through van der Waals interactions. As shown in TableA2, specific atoms of compound (54) interact with specific atoms of HIS483, PHE 529, PRO 608, SER 611, ASP 627, SER 628, CYS 629, SER 633, SER654, TRP 655, GLY656, SER 657, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (2018) through van der Waals interactions. As shown inTable A2, specific atoms of compound (2018) interact with specific atomsof HIS 483, PHE 529, TYR 607, ASP 627, SER 628, CYS 629, ARG 630, SER633, SER 654, TRP 655, GLY656, SER 657, CYS 660, GLN 665, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1149) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1149) interact with specific atomsof HIS 483, ASP 526, GLY 528, PHE 529, PRO 608, SER 611, ASP 627, SER628, CYS 629, SER 633, SER 654, TRP 655, GLY656, SER 657, MET 658, CYS660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1031) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1031) interact with specific atomsof HIS 483, PHE 529, TYR 607, SER 611, ASP 627, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1153) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1153) interact with specific atomsof HIS 483, PHE 529, ASP 627, SER 628, CYS 629, ARG 630, SER 633, VAL653, SER 654, TRP 655, GLY656, SER 657, MET 658, CYS 660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1025) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1025) interact with specific atomsof HIS 483, PHE 529, TYR 607, ASP 627, SER 628, CYS 629, SER 633, SER654, TRP 655, GLY656, SER 657, MET 658, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1012) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1012) interact with specific atomsof HIS 483, PHE 529, PRO 606, TYR 607, PRO 608, SER 628, CYS 629, ARG630, SER 633, SER 654, TRP 655, GLY656, SER 657, MET 658, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1078) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1078) interact with specific atomsof HIS 483, PHE 529, PRO 608, SER 611, ASP 627, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, MET 658, GLY 667, andTYR 669

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1145) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1145) interact with specific atomsof HIS 483, PHE 529, TYR 607, SER 611, ASP 627, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658, CYS660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1050) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1050) interact with specific atomsof PHE 529, TYR 607, PRO 608, ASP 627, SER 628, CYS 629, ARG 630, SER633, VAL 653, SER 654, TRP 655, GLY656, SER 657, CYS 660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1253) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1253) interact with specific atomsof HIS 483, PHE 529, TYR 607, SER 611, SER 628, CYS 629, ARG 630, SER633, VAL 653, SER 654, TRP 655, GLY656, SER 657, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1257) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1257) interact with specific atomsof HIS 483, PHE 529, PRO 606, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1297) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1297) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, and SER 657.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1304) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1304) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1306) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1306) interact with specific atomsof HIS 483, PHE 529, TYR 607, PRO 608, SER 611, ASP 627, SER 628, ARG630, SER 633, SER 654, TRP 655, GLY656, SER 657, CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1307) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1307) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, ASP 627, SER628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER657, MET 658, CYS 660, GLY 667, and TYR 669

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1328) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1328) interact with specific atomsof HIS 483, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1334) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1334) interact with specific atomsof HIS 483, PHE 529, TYR 607, PRO 608, SER 611, ASP 627, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, CYS 660, GLY667, and TYR 669.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1335) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1335) interact with specific atomsof HIS 483, PHE 529, TYR 607, PRO 608, ASP 627, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, CYS 660, GLN665, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1338) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1338) interact with specific atomsof HIS 483, ALA 527, GLY 528, PHE 529, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET658, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1345) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1345) interact with specific atomsof HIS 483, PHE 529, LEU 575, SER 611, ASP 627, SER 628, CYS 629, ARG630, SER 633, SER 654, TRP 655, GLY656, SER 657, MET 658, CYS 660, GLN665, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1351) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1351) interact with specific atomsof HIS 483, ALA 527, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER657, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1353) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1353) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, andMET 658.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1360) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1360) interact with specific atomsof HIS 483, GLY 528, GLY 528, PHE 529, PRO 606, TYR 607, PRO 608, SER611, SER 628, CYS 629, ARG 630, SER 654, TRP 655, GLY656, and SER 657.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1367) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1367) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, and SER 657.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1368) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1368) interact with specific atomsof HIS 483, PHE 529, PRO 606, TYR 607, SER 611, SER 628, CYS 629, ARG630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET 658, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1371) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1371) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, ASP 627, SER628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER657, MET 658, CYS 660, GLY 667, and TYR 669.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1372) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1372) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1373) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1373) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, andCYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1492) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1492) interact with specific atomsof HIS 483, PHE 529, PRO 606, ASP 627, SER 628, CYS 629, ARG 630, SER633, VAL 653, SER 654, TRP 655, GLY656, SER 657, CYS 660, and GLY 667.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1399) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1399) interact with specific atomsof HIS 483, ALA 527, GLY 528, PHE 529, TYR 607, PRO 608, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, and SER 657.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1406) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1406) interact with specific atomsof HIS 483, ASP 526, ALA 527, GLY 528, PHE 529, TYR 607, PRO 608, SER628, CYS 629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER657, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1411) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1411) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET658, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1433) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1433) interact with specific atomsof HIS 483, PHE 529, TYR 607, ASP 627, SER 628, CYS 629, ARG 630, SER633, VAL 653, SER 654, TRP 655, GLY656, MET 658, GLY 667, and TYR 669.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1435) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1435) interact with specific atomsof HIS 483, PHE 529, TYR 607, ASP 627, SER 628, CYS 629, ARG 630, SER633, VAL 653, SER 654, TRP 655, GLY656, GLY 667, and TYR 669.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1441) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1441) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, PRO 608, SER 611, SER 628, CYS629, ARG 630, SER 633, VAL 653, SER 654, TRP 655, GLY656, SER 657, MET658, and CYS 660.

The crystal structure showed that MASP-2 CCP2-SP amino acids interactwith compound (1450) through van der Waals interactions. As shown inTable A2, specific atoms of compound (1450) interact with specific atomsof HIS 483, GLY 528, PHE 529, TYR 607, ASP 627, SER 628, CYS 629, SER654, TRP 655, GLY656, SER 657, CYS 660, GLY 667, and TYR 669.

Example 313. MASP-2 Specificity Over Thrombin

The crystallographic structure of thrombin in complex with melagatran(Protein Data Bank accession code 4BAH) was compared to thecrystallographic structure of MASP-2 in complex with melagatran and tothat with other compounds.

The X-ray crystallographic structure of human alpha-thrombin in complexwith compound (1334) was also determined as described by Biela et al.,J. Med. Chem 2012, 55, 6094-6110, to a resolution of 1.8A in space groupC 1 2 1 and compared to the crystallographic structure of MASP-2co-crystallized with compound (1334).

Overlays were created with MatchMaker functionality in Chimera software(Pettersen et al., 2004), using the respective serine protease domainsfor iterative matching.

Thrombin melagatran co-structure (4BAH) overlaid with the co-structureof compound 1065 with MASP-2.

The thrombin co-structure with compound (1334) (using numberingaccording to PDB Protein Data Bank accession code 1K22) was overlaidwith the co-structure of a compound of this disclosure with MASP-2 (see,FIG. 61-63 ). FIG. 63 clearly shows that the elongated and bulky M4 ofthe MASP-2 inhibitor not being accommodated and reversing theorientation of the pyrrolidine and benzyl moiety of compound (1334).

It was found that thrombin possesses a ridge, made up of residues GLU130 and ILE 209 (ASN98, LEU99 and ILE 174), creating a barrier for largebulky residues to occupy this site (see, FIG. 61-63 ). In thecorresponding region in MASP-2 however, a crevice exists that is linedby amino acids PHE 529, GLY 528, TRP 655, SER 611, PRO 608, TYR 607, andPRO 606. FIG. 61 , FIG. 65 . Crucially, there is no correspondingbarrier to large bulky residues in MASP-2, hence allowing large bulkyresidues to bind and, providing a means to design specificity for MASP-2over thrombin and other similar proteases.

As discussed, compounds of the disclosure may have specificity forMASP-2 over that of thrombin. MASP-2 has a V-shaped crevice that extendsout of the S3 and S4 binding pocket. Compounds can reach into thiscrevice and form productive van der Waals interactions with bulkyaromatic residues in the M4 region. The corresponding area in thrombinis blocked however, by ridge-forming residues GLU 130 and ILE 209 (GLU259, ASN98, LEU99 and ILE 209). FIG. 61 , FIG. 65 .

As discussed, compounds of the disclosure may have specificity forMASP-2 over that of thrombin. MASP-2 has a S1 indentation extendinginside the S1 binding pocket. Compounds can reach into this crevice andform productive van der Waals interactions with CYS629, CYS660 residuesthat interact with the M₁ region. The corresponding area in thrombin isblocked however, by ridge-forming residues CYS220 and GLY219 (1k22).

As discussed, compounds of the disclosure may have specificity forMASP-2 over that of thrombin. MASP-2 has a S2 shelf extending the S1binding pocket. Compounds can reach into this crevice and formproductive van der Waals interactions with LEU99, SER654, HIS483,residues in the M₃ region. The corresponding area in thrombin is blockedhowever, by ridge-forming residues TYR60A and LYS60F (1k22).

As discussed, compounds of the disclosure may have specificity forMASP-2 over that of thrombin. MASP-2 has a S3 entry indentation the S3binding area. Compounds can reach into this crevice and form productivehydrogen bond interactions with GLY656, a residue in the M₃ region. Thecorresponding area by residue GLY 216 (1k22) in thrombin is displaced ascompared to the corresponding residue GLY656 in MASP-2.

Based on the experimentally determined interactions of compounds withMASP-2, it is evident that H-bonds are preferentially formed withresidues ASP627, SER628, SER654, GLY656, GLN 665, ARG630, PRO606, SER633, CYS660 and SER 657, ionic/electrostatic interactions with ASP627 orARG 630, via a water molecule as well as additional van der Waalscontacts with ALA 468, ALA469, HIS 483, ASP526, ALA527, GLY528, PHE 529,LEU575, PRO 606, TYR 607, PRO608, SER 611, ASP627, SER 628, CYS 629, ARG630, GLY 631, ASP 632, SER 633, GLY634, GLY 635, VAL 653, SER 654, TRP655, GLY656, SER 657, MET 658, ASN 659, CYS 660, GLN 665, GLY 667, TYR669.

REFERENCES

-   Ambrus, G., Gál, P., Kojima, M., Szilágyi, K., Balczer, J., Antal,    J., Gráf, L., Laich, A., Moffat, B. E., Schwaeble, W., Sim, R. B.,    and Závodszky, P. Natural Substrates and Inhibitors of    Mannan-Binding Lectin-Associated Serine Protease-1 and -2: A Study    on Recombinant Catalytic Fragments J. Immunol. 170, 1374-1382    (2003).-   Harmat V, Gál P, Kardos J, Szilágyi K, Ambrus G, Végh B, Náray-Szabó    G, Závodszky P. The structure of MBL-associated serine protease-2    reveals that identical substrate specificities of C₁ s and MASP-2    are realized through different sets of enzyme-substrate    interactions. J Mol Biol. 2004 Oct. 1; 342(5):1533-46.-   Gál P, Harmat V, Kocsis A, Bián T, Barna L, Ambrus G, Végh B,    Balczer J, Sim RB, Náray-Szabó G, Závodszky P. J Biol Chem. 2005    Sep. 30; 280(39):33435-44. Epub 2005 Jul. 21. A true autoactivating    enzyme. Structural insight into mannose-binding lectin-associated    serine protease-2 activations.-   Laskowski R A, Swindells M B (2011). LigPlot+: multiple    ligand-protein interaction diagrams for drug discovery. J. Chem.    Inf. Model., 51, 2778-2786.-   Paul Emsley, Bernhard Lohkamp, William G. Scott, Kevin Cowtan    Features and Development of Coot. Acta Crystallographica Section    D—Biological Crystallography (2010) 66, 486-501.-   UCSF Chimera—a visualization system for exploratory research and    analysis. Pettersen E F, Goddard T D, Huang C C, Couch G S,    Greenblatt D M, Meng E C, Ferrin T E. J Comput Chem. 2004 October;    25(13):1605-12.

Example 314. Testing the Virtual Binding Site Identification Method

To evaluate the utility of the crystallographically determinedMASP-2-CCP2-SP small molecule inhibitor compound co-structures for theidentification of virtual binding sites of HTS hit compounds, apreliminary control experiment was carried out according to the virtualbinding site identification process of the invention.

The crystallographically determined MASP-2 structure with bound 1030(FIG. 10 ) was prepared for docking by producing an initial MASP-2 modelaccording to Step 1 (FIG. 76 ). As such, the CCP2 chain, sulfate ions,the polyethylene glycol molecule, the 307 water molecules, and the bound1030 molecule were removed from the experimental crystallographicstructure parameters in the PDB file, followed by reproducing themodified crystal structure as an initial MASP-2 model using ICM Prosoftware (Abagyan & Totrov, 1994 and Abagyan et al., 1994).

In accordance with Step 2 of the inventive method, during the conversionfrom PDB filetype to an ICM object, the MASP-2 model is optimized byadding hydrogens and optimizing the following amino acids: His, Pro,Asn, Gln, Cys. As a next step, a portion of the surface area (ca. ⅓ ofthe molecular surface of the MASP-2 SP domain) around the S1 bindingsite is defined, and internal surfaces are excluded using the ICM pocketfinder tool, using a tolerance setting of 1. This procedure yields asurface area of approx. 2,300 square Angstrom. Then, a MASP-2 receptormap is calculated for a box that confines the docking calculation toonly ⅓^(rd) of the protein surface.

Step 3 involves converting digital representations for small molecule1030 (FIG. 10 ) and small molecule (1024) (FIG. 3 ) as energy minimizedthree dimensional digital representations. The digital representationsfor 1030 and 1024 are reproduced below:

The 3D representations for 1030 and 1024 were prepared by loading thestructure-data file (SDF) format representations for each compound,followed by computationally building the hydrogens for each compound,assigning charges, and, finally, converting the compounds into 3Dmolecules and subsequently used in virtual docking calculations (Step4). Virtual docking calculations using ICM Pro software were performedwith effort settings of 1 or 2 and resulting location, orientation andposes were compared with crystallographically determined to those of thesame molecule.

Re-docking of 1030 into the crystal structure of MASP-2 bound to 1030re-produces the pose with a score of −38.46 and an RMSD of 1.75 Å. Thecross-docking of 1024 into the crystal structure of MASP-2 bound to 1030was performed and compared to the overlayed crystallographicallydetermined 1024 molecule in MASP-2 re-produces the pose with a score of−35.41 and an RMSD of 0.577 Å.

The MASP-2 contacts with hydrogen bonding residues and atoms of ASP 627(OD2), Ser 628 (O), SER 654 (O), GLY 656 (N) and SER 657 (O) werereproduced for the cross-docked compound 1024, confirming that theinteraction of small molecules from Table A1 with affinity andinhibitory capacity can also be predicted computationally with highaccuracy.

Example 315. Interaction of MASP-2 with Peptide SGMI-2

Heja et al. (2012) describe the interaction of a 38-mer peptide (SGMI-2)with the serine protease domain of MASP-2. In their reportedhigh-resolution crystallographic structure of SGMI-2 bound to MASP-2(Protein Data Bank accession code 3TJV), H-bonding analysis herein(using distance cutoff as defined above) depicts hydrogen bondingresidues and respective atoms for MASP-2 amino acids GLY 464 (O-atom),GLY 465 (O atom), Thr (N, O and OG1 atom), PRO 606 (O atom), ARG 609 (OGatom), ASP 627 (O atom), SER 628 (O and OG atoms), GLY 631 (N atom), SER633(N and OG atom), GLY 656 (N and O atom) and the N atom of MET 657binding via H-bonds to SGMI-2. Notably, hydrogen bonds are notestablished between the SGMI-2 peptide and MASP-2 oxygen atom O of SER654, the oxygen atoms O and OG of SER 657, the sulfur atom of CYS 660nor with the oxygen atoms O and OE1 of GLN 665.

Furthermore, in their reported high-resolution crystallographicstructure (Protein Data Bank accession code 3TJV), van der Waals bondinganalysis herein (using distance cutoff as defined above) reveals thebinding of MASP-2 amino acid atoms to certain atoms of SGMI-2, utilizingMASP-2 Carbon atom C and oxygen atom O of Gly 464, Carbon atoms C, CA,CB, CG2 and Nitrogen atom N and oxygen atoms O and OG1 of Thr 467,Carbon atom CB of Alanine 468, Carbon atoms CE1 and CG and Nitrogen atomND1 of His 483, Carbon atoms CA and CB of Ala 484, Oxygen atom O of His525, Carbon atom O and Oxygen atom O of Asp 526, Carbon atom CA of Ala527, Nitrogen atom N of Gly 528, Carbon atom CD1 of Leu 575, Carbonatoms CD1, CD2, CG and Nitrogen atom of Leu 581, Carbon atom CE2 of Tyr601, Carbon atom CA of PRO 606, Carbon atom C and Oxygen atom O of Arg609, Carbon atom C of Gly 610, Carbon atom CA and Nitrogen atom N of Ser611, Carbon atom C and CB and Oxygene atom O of ARG 630, Carbon atoms Cand CA and Nitrogen atom N of Gly 631, Nitrogen atom N and Carbon atomsCA and CB of Asp 632, Carbon atoms CB and CE of Met 658, as well asCarbon atom CD2 and Nitrogen atom NE2 of Histidine 483, Carbon atomsCE1, CD2 and CZ of Phe 529, Carbon atoms C, CB, CG and oxygen atom ofPRO 606, Carbon atom CD2 of Tyr 607, Carbon atoms CB and CG of PRO 608,oxygen atom OG of Ser 611, Oxygen atom OD1 of ASP 627, Carbon atom Coxygen atoms O and OG of Ser 628, Carbon atoms CA, CD, CG of ARG 630,oxygen atom OG and Carbon atom CG1 of Ser 633, Carbon atom CG1 of Val653, Oxygen atom O of Ser 654, Carbon atoms C, CA, CB, CE3, CZ3 andOxygen atom O of Trp 655, Nitrogen atom N and Oxygen atom O of Gly 656,Nitrogen atom of Met 658 and Carbon atom CA of Gly 667. Notably, van derWaals interactions are not established between the SGMI-2 peptide andMASP-2 Carbon atoms C and CA of ALA 468, carbon atom CA of ALA 469,carbon atom CA of ASP 526, Carbon atom C and Oxygen atom O of ALA 527,nitrogen atom N and carbon atom CA of GLY528, Carbon atoms CD2 and CE1of PHE 529, OH atom of TYR 607, carbon atom CB of SER 611, Carbon atomCG and oxygen atom OD2 of SER 628, Carbon atoms C, CA, CB and nitrogenatom N of CYS 629, Carbon atom CZ and nitrogen atom NE2 of ARG 630, Catom of GLY 631, Carbon atoms C, CA and CB as well as oxygen atom O ofASP 632, Carbon atoms C and CA as well as nitrogen atom N of GLY634,Nitrogen atom N of GLY 635, carbon atom CB and oxygen atom O of VAL 653,carbon atom CH2 of TRP 655, Carbon atom CB and oxygen atom OG of SER657, Carbon atom CA, C and CE as well as oxygen atom O of MET658, Carbonatom C and nitrogen atom N of GLY 667, carbon atom CE2 of TYR669, C andCA, Nitrogen and oxygen atom of SER657, Carbon atom C of Asparagine 659,Carbon atom CA, CB and Sulphur atom SG of Cysteine 660, Carbon atom CDand Oxygen atom OE1 of Glutamine 665, Tyrosine 669 carbon atoms CZ2 andCE1.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. Each reference, including withoutlimitation all patent, patent applications, and publications, cited inthe present application is incorporated herein by reference in itsentirety for all purposes.

TABLE A1 (H-Bonds) Amino Acid ASP SER ARG SER GLY MASP-2 AA# 627 628 630654 656 AA atom OD1 OD2 O O OG OG NE NH1 NH1 O O N 1 1097 2.74 3.03 2.812.98 3.12 N5 N5 N4 N1 O2 D D D D A 2 1024 2.74 2.79 2.86 3.06 N4 N4 N3O2 D D D A 3 1036 2.96 2.9  2.8  3.22 N27 N27 N17 029 D D D D 4 10812.86 2.81 2.92 N27 N17 N03 D D D 5 1063 2.93 2.94 3.25 N4 N3 O1 D D A 61065 3.14 3.08 2.92 3.31 N29 N28 N14 O09 D D D A 7 1030 3.17 2.82 2.823.12 N5 N3 N1 O2 D D D A 8 1037 2.91 2.89 3.35 N19 N09 O04 D D A 9 11183.18 2.88 2.77 3.07 N5 N3 N1 O1 D D D A 10 Melagatran 2.75 999 N24 D 111129 2.79 2.86 2.84 2.93 N19 N19 N10 O07 D D D A 12 1034 2.9  2.91 2.992.91 N20 N20 N10 O07 D D D A 13 1088 2.91 3.16 3.16 2.89 3.22 N31 N29N31 N01 O07 D D D D A 14 1059 2.99 2.95 2.95 2.94 3.13 N4 N6 N1 N3 O2 DD D A 15 1007 3.27 2.59 2.94 N5 N1 N2 D D D 16 1090 2.8  2.96 2.78 3.3 N4 N2 N1 O2 D D D A 17 1089 2.8  2.93 2.82 3.3  N4 N3 N1 O2 D D D A 181021 2.99 3.08 N1 O1 D A 19 1297 3.13 2.96 2.88 2.67 3.33 N5 N4 N3 N1 O1D D D D A 20 1304 3.17 3.18 2.97 2.81 3.2  N5 N4 N3 N2 O1 D D D D A 211306 2.6  2.24 2.69 3.05 N4 N4 N2 O1 D D D A 22 1307 2.91 2.86 2.95 N3N2 O1 D D A 23 1328 3.06 2.67 2.82 3.33 N4 N3 N2 O1 D D D A 24 1334 2.812.83 3.16 N3 N2 O1 D D A 25 1335 3.21 2.99 2.77 3.08 N5 N1 N3 O1 D D D A26 1338 3.2  3.04 2.99 2.78 3.23 N5 N4 N3 N2 O1 D D D D A 27 1345 2.642.37 3.02 3.13 3.05 N5 O1 N1 N3 O2 D A D D A 28 1351 3.22 2.98 2.76 3.25N5 N3 N2 O1 D D D A 29 1353 3.17 3    2.85 3.15 N5 N3 N1 O1 D D D A 301367 3.15 3.15 3.08 2.77 3.15 N4 N3 N2 N6 O2 D D D D A 31 1368 3.24 3.163.04 3.07 N38 N34 NO1 O29 D D D A 32 1371 2.86 2.75 3.18 N3 N2 O1 D D A33 1372 3.17 3.18 2.97 2.81 3.23 N4 N3 N2 N5 O2 D D D D A 34 1373 3.213.18 3.04 2.76 3.2  N5 N4 N3 N2 O1 D D D D A 35 1492 3.32 2.78 2.7  3.06N7 N4 N3 O1 D D D A 36 1399 3.26 3.15 3.04 2.75 3.21 N5 N4 N3 N1 O2 D DD D A 37 1406 3.22 2.96 2.76 3.28 N5 N3 N2 O1 D D D A 38 54 2.81 2.74N11 O09 A A 39 2018 3.01 2.94 3.26 N5 N3 O2 D D A 40 1031 2.18 2.83 2.67O04 O09 N11 A A D 41 1153 3.27 2.96 2.3  2.84 2.96 N1 N2 O1 N5 O2 D D AD A 42 1025 3.11 2.38 3.17 N09 N05 N09 D D D 43 1012 3.18 2.93 2.77 3.18N5 N3 N1 O2 D D D A 44 1078 2.92 3.25 2.66 3.14 O2 N2 N1 O1 A D D A 451145 2.84 2.84 2.58 3.09 N4 N1 N3 O2 D D D A 46 1050 3.03 2.58 3.18 N2N5 O2 D D A 47 1253 3.33 3.12 2.99 2.83 3.23 N07 N01 N10 N22 O17 D D D DA 48 1257 3.12 3.02 2.82 N01 N10 N18 D D D 49 14 50 1042 3.32 2.74 2.34N22 N22 N03 D D D 51 1433 2.89 2.75 3.13 N3 N5 O2 D D A 52 1360 3.153.18 3.04 2.9  3.21 N5 N3 N4 N2 O1 D D D D A 53 1450 2.97 2.78 3.04 N3N2 O1 D D A 54 1435 3.32 3.01 2.79 3.26 N5 N3 N2 O1 D D D A 55 1441 3.233.06 3.07 3.2  N5 N4 N1 O1 D D D A 56 1411 3.17 3.2  2.66 3.06 3.07 N5N4 O3 N1 O2 D D A D A 57 1149 3.09 2.7  3.24 N1 N3 O2 D D A Amino AcidSER GLN SER PRO HIS ALA CYS MASP-2 AA# 657 665 633 606 483 469 660 AAatom O OG O OE1 OE1 OG O NE2 N SG  1 1097 2.74 N6  D  2 1024 2.94 N5  D 3 1036 2.93 N26 D  4 1081 2.69 N26 D  5 1063 2.83 N5  D  6 1065  7 10302.91 N4  D  8 1037 2.85 N18 D  9 1118 2.93 N4  D 10 Melagatran 2.84 999N25 D 11 1129 2.92 2.76 N20 N20 D D 12 1034 2.75 3.26 2.8  N19 N20 N19 DD D 13 1088 14 1059 2.77 2.94 3.31 N5  N6  N6  D D D 15 1007 2.88 N5  D16 1090 2.73 N5  D 17 1089 2.93 N5  D 18 1021 19 1297 3.06 N5  D 20 13042.96 N5  D 21 1306 2.87 N5  D 22 1307 23 1328 2.44 N5  D 24 1334 25 13352.85 2.73 N6  N6  D D 26 1338 2.93 N5  D 27 1345 3.01 2.63 N6  N6  D D28 1351 2.8  N5  D 29 1353 2.91 N5  D 30 1367 2.88 N4  D 31 1368 2.943.21 N38 N17 D D 32 1371 2.96 C23 D 33 1372 2.87 N4  D 34 1373 2.89 N5 D 35 1492 2.72 2.62 N5  N7  D D 36 1399 2.86 N5  D 37 1406 2.78 N5  D 3854 2.57 N15 D 39 2018 2.84 2.56 3.08 N4  N4  N3  D D A 40 1031 41 11532.98 N1  D 42 1025 43 1012 2.89 N5  D 44 1078 45 1145 2.81 N5  D 46 10502.86 N4  D 47 1253 2.85 N07 D 48 1257 2.86 N08 D 49 14 2.89 3    O2 O7 DD 50 1042 2.65 N21 D 51 1433 52 1360 2.96 N5  D 53 1450 54 1435 2.84 N5 D 55 1441 2.91 N5  D 56 1411 2.61 N5  D 57 1149 2.75 3.19 3.16 N2  N2 N2 D D D

TABLE A2 TABLE A2-1: van der Waals Amino Acid ALA ALA HIS ASP MASP-2 AA#468 469 483 526 AA atom C CA CB CA CD2 CE1 NE2 C CA O 1 1129 3.75 C02 21034 3 1024 3.39 C21 4 1059 3.69 C14 5 1088 6 1036 3.81 C28 7 1081 3.74C29 8 1063 9 1065 3.67 C30 10 1030 3.61 C22 11 1037 12 1118 3.64 C8  131007 3.38 C8  14 Melagatran 999 15 1090 3.74 C19 16 1089 3.71 3.83 C24C24 17 1021 3.51 3.58 C20 C20 18 1097 3.63 3.53 C23 C23 19 54 20 10423.56 C29 21 2018 3.7  3.87 N6  C16 22 1031 3.57 3.62 3.17 C07 C07 C07 231153 3.83 C11 24 1025 3.68 3.81 O28 O28 25 1012 3.63 3.57 C20 C20 261078 3.35 3.28 C15 C15 27 1145 3.75 C22 28 1050 29 1253 3.74 3.66 C29C29 30 1257 3.7  3.72 C29 C29 31 1297 3.74 3.84 C18 C20 32 1304 3.713.65 C14 C14 33 1306 3.47 3.32 C14 C14 34 1307 3.5  C14 35 1328 3.793.73 C14 C14 36 1334 3.66 3.84 C14 N3  37 1335 3.72 3.7  3.58 3.84 C20C22 N4 C20 38 1338 3.58 3.82 C18 C18 39 1345 3.69 3.37 C3  C3  40 13513.66 3.9  C20 C20 41 1353 3.77 3.67 C23 C23 42 1367 3.71 3.59 C12 C12 431368 3.86 3.67 C04 C04 44 1371 3.55 3.61 C14 C14 45 1372 3.77 3.67 C2 C2  46 1373 3.71 3.62 C14 C14 47 1492 3.78 3.84 3.68 C13 C13 C14 48 13993.72 3.6  C26 C26 49 1406 3.7  3.67 3.55 3.89 3.69 C15 C15 C26 C26 C2650 1433 3.73 3.76 C23 C23 51 14 3.69 3.52 3.52 3.89 3.72 3.84 3.78 33.59 O7 O7 O7 O7 O5  C15 C8 O2 O5 52 1360 3.76 3.69 C19 C19 53 1450 3.9 3.88 C14 C14 54 1435 3.7  3.6  C14 C14 55 1441 3.74 3.61 C18 C18 56 14113.51 3.46 C2  C2  57 1149 3.81 3.29 3.87 C11 C27 C28 TABLE A2-2: van derWaals Amino Acid ALA GLY MASP-2 AA# 527 528 AA atom C CA O CA N 1 1129 21034 3 1024 4 1059 5 1088 6 1036 7 1081 8 1063 9 1065 10 1030 11 1037 121118 13 1007 14 Melagatran 999 15 1090 16 1089 17 1021 18 1097 19 543.87 C17 20 1042 21 2018 22 1031 23 1153 24 1025 25 1012 26 1078 27 114528 1050 29 1253 30 1257 31 1297 3.76 3.61 3.39 C15 C14 C15 32 1304 3.79C11 33 1306 34 1307 3.75 C11 35 1328 36 1334 37 1335 38 1338 3.67 3.333.32 3.72 3.32 3.84 C16 C16 C17 C15 C16 C17 39 1345 40 1351 3.59 3.353.71 3.51 3.72 3.66 3.68  3.81 3.9  3.79 3.8  3.42 3.5  C17 C18 C18 C17C18 C14 C15 C16 C18 C19 C17 C18 C19 41 1353 3.52 3.81 C10 C9  42 13673.78 3.52 C18 C19 43 1368 44 1371 3.8  C11 45 1372 3.83 C19 46 1373 3.79C11 47 1492 48 1399 3.73 3.49 3.72 3.8  3.71 3.79 3.69 3.45 3.84  3.873.49 3.75 3.61 3.53 3.67 3.81 3.86 C12 C13 C14 C12 C13 C13 C14 C10 C11C14 C15 C10 C11 C12 C13 C14 C15 49 1406 3.68 3.83 3.71 3.75 3.56 3.51C25 C25 C12 C24 C24 C25 50 1433 51 14 52 1360 3.79 3.31  3.82 C12 C13C14 53 1450 3.89 C10 54 1435 55 1441 3.71 C15 56 1411 3.85 C13 57 11493.61 3.49 C3.72 3.76 3.4  C29 C31 N6  O3  C29 TABLE A2-3: van der WaalsAmino Acid PHE MASP-2 AA# 529 AA atom CD1 CD2 CE1 CE2 CZ 1 1129 3.523.68 3.86 3.84 C30 N04 C03 C01 2 1034 3.7  3.41 3.71 3.69 N04 C03 C02C01 3 1024 3.85 3.58 3.46 3.7 3.8 3.87 3.79 3.74 C7  C6  C6  C5  C4  C21C11 N2  4 1059 3.9  3.61 3.72 3.8  3.76 3.71 C13 C8  C7  C14 N2  C2  51088 3.62 3.66 3.52 3.64 3.86 3.54 3.83 3.71 3.59 C13 C12 C06 C19 C04C19 C13 N05 C04 6 1036 3.72 3.45 3.84 C14 N13 C06 7 1081 3.38 3.4  3.583.49 3.64 3.71 3.62 3.58 3.7  C16 C16 C08 C07 C29 C09 C29 C09 N04 8 10633.71 3.51 3.63 3.66 3.56 3.54 3.44 3.34 C15 C15 C2  C10 C8  C10 C8  N2 9 1065 3.69 3.85 3.86 3.76 3.72 3.66 3.56 C30 C11 C19 C02 C30 C11 N10 101030 3.56 3.7  3.86 3.51 3.4  3.3  C22 C12 N2  C22 C12 N2  11 1037 3.273.49 3.73 3.78 3.37 3.85 C20 C13 C20 C05 N03 C01 12 1118 3.52 3.76 3.8 3.79 3.72 3.63 C13 C8  C6  C8  C6  N2  13 1007 3.83 3.58 3.6  3.75 3.893.88 3.74 3.85 3.81 3.62 3.82 C16 C18 C17 C16 C15 C14 C13 C8  C7  N3 C7  14 Melagatran 3.48 3.8  3.87 3.73 999 C27 C26 C12 N11 15 1090 3.873.57 3.61 3.84 C18 C18 N3  C19 16 1089 3.83 3.81 3.86 3.56 3.68 3.663.85 C12 C24 C9  C10 N2  C12 C24 17 1021 18 1097 3.79 3.88 N3  C13 19 5420 1042 3.64 3.24 3.57 C09 C29 C29 21 2018 3.68 3.74 3.85 3.55 C11 C16C7  N1  22 1031 3.75 C07 23 1153 3.36 3.48 3.58 3.05 3.57 2.93 3.87 3.08C17 C18 C16 C17 C18 C11 C10 C11 24 1025 3.74 3.8  3.55 3.67 3.25 3.563.88 C21 C22 C15 C20 C21 C22 C15 25 1012 3.75 3.78 3.72 3.79 3.54 C20C4  C12 C20 N2  26 1078 3.85 3.61 3.87 3.87 3.85 3.88 3.8  3.82 C14 C8 C9  C15 C2  C2  C8  N2  27 1145 3.54 3.69 3.51 3.67 3.78 3.88 3.75 3.883.69 C12 C12 C6  C7  C15 C2  C2  C22 N2  28 1050 3.61 3.56 3.88 C17 C17N1  29 1253 3.7  3.86 3.77 3.82 3.81 3.65 C18 C24 C29 C12 C29 N14 301257 3.89 3.79 3.88 3.82 C28 C12 C29 N14 31 1297 3.67 3.5  3.77 3.673.82 C11 C2  C6  C2  N2  32 1304 3.79 3.85 3.75 3.84 3.84 3.84 3.71 3.813.55 C12 C1  C14 C11 C12 C4  C1  C14 N1  33 1306 3.88 3.82 3.63 C10 C11N1  34 1307 3.69 3.74 3.9  3.86 C10 C10 C4  N1  35 1328 3.78 3.8  3.763.81 3.61 3.65 3.69 3.75 C12 C11 C12 C1  C14 C1  C14 N1  36 1334 3.733.76 3.6  3.7  3.88 3.7  3.81 3.69 C12 C11 C14 C12 C13 C1  C14 N1  371335 3.75 3.58 3.8  3.85 C15 C15 C20 C20 38 1338 3.84 3.72 3.86 3.763.51 C1  C18 C4  C1  N1  39 1345 3.51 3.7  3.71 3.88 C18 C19 C23 N2  401351 3.8  3.83 3.59 3.7  3.69 3.45 C4  C1  C20 C1  C20 N1  41 1353 3.683.84 3.7  3.82 3.71 3.6  3.65 3.54 C9  C14 C23 C8  C9  C14 C23 N2  421367 3.8  3.76 3.87 3.64 3.86 3.8  3.68 3.39 C20 C12 C3  C13 C20 C12 C3 N1  43 1368 3.76 3.43 3.34 3.51 3.7  3.79 3.71 C23 C28 C22 C23 C28 C04C04 44 1371 3.86 3.89 3.84 3.61 C10 C4  C1  N1  45 1372 3.74 3.81 3.843.69 3.89 3.88 3.61 3.68 3.45 C18 C19 C1  C2  C18 C19 C1  C2  N1  461373 3.79 3.84 3.88 3.75 3.88 3.82 3.81 3.7  3.77 3.47 C11 C12 C1  C14C10 C11 C4  C1  C14 N1  47 1492 3.73 3.89 C1  C13 48 1399 3.85 3.89 3.7 3.7  3.71 3.76 3.47 C7  C17 C26 C2  C17 C26 N2  49 1406 3.63 3.74 3.643.84 3.8  3.73 3.82 3.73 3.69 3.45 C11 C12 C15 C2  C11 C12 C5  C15 C2 N1  50 1433 3.77 3.82 3.76 3.78 3.73 C23 C13 C10 C23 N4  51 14 3.21 3.473.86 3.1  O5  N2  O4  O5  52 1360 3.78 3.72 3.75 3.59 C19 C1  C19 N1  531450 3.86 3.58 3.76 3.89 3.6  3.47 3.63 C13 C14 C10 C11 C13 C14 N1  541435 3.61 3.88 3.7  3.66 3.71 3.51 Cl2 C1  C14 C1  C14 N1  55 1441 3.853.87 3.61 3.89 3.7  C18 C12 C7  C18 N2  56 1411 3.69 3.71 3.59 3.83 3.63C2  C11 C6  C2  N2  57 1149 3.68 3.78 3.53 3.8  3.34 C11 C27 C28 C10 C11TABLE A2-4: van der Waals Amino Acid LEU PRO TYR MASP-2 AA# 575 606 607AA atom CD1 C CB CG CD O CA CD1 CD2 1 1129 3.86 C28 2 1034 3.71 3.333.41 C28 C28 C27 3 1024 3.9  C8  4 1059 3.89 C13 5 1088 3.89 3.88 2.973.79 3.82 C16 C17 C16 C15 C16 6 1036 7 1081 8 1063 9 1065 10 1030 111037 3.89 3.49 3.73 C28 C28 C27 12 1118 3.79 C27 13 1007 3.84 C14 14Melagatran 3.72 999 C5  15 1090 3.36 3.3  C7  C8  16 1089 3.85 3.62 3.4 C7  C8  C7  17 1021 18 1097 3.74 3.84 3.82 3.33 3.79 3.8  3.61 3.73 C10C9  C9  C10 C10 C8  C9  C10 19 54 20 1042 21 2018 3.9  3.56 3.77 C12 C13C14 22 1031 3.85 C15 23 1153 24 1025 25 1012 3.85 3.33 3.86 C9  C8  C9 26 1078 27 1145 3.89 C9  28 1050 3.82 3.74 C20 C21 29 1253 30 1257 3.383.83 3.72 3.82 C26 C24 C25 C26 31 1297 3.81 C7  32 1304 3.78 C7  33 13063.85 C7  34 1307 3.83 C7  35 1328 3.86 3.68 C13 C7  36 1334 3.81 C7  371335 3.84 3.84 C18 C19 38 1338 39 1345 3.59 3.66 3.8  C14 N4  O1  401351 41 1353 3.75 C6  42 1367 43 1368 3.6  3.44 3.74 3.75 C15 C15 C16C18 44 1371 3.79 3.81 3.6  C7  C8  C9  45 1372 3.77 3.77 C16 C17 46 13733.82 3.81 C13 C7  47 1492 3.81 C9  48 1399 3.7  C5  49 1406 3.74 C8  501433 51 14 52 1360 3.83 3.75 C16 C17 53 1450 3.44 C12 54 1435 3.83 C7 55 1441 3.8  C9  56 1411 3.8  C8  57 1149 TABLE A2-5: van der WaalsAmino Acid TYR PRO SER MASP-2 AA# 607 608 611 AA atom CE1 CE2 OH CD CGCA 1 1129 2 1034 3 1024 3.54 3.69 C9  C8  4 1059 3.89 C12 5 1088 3.73C15 6 1036 7 1081 8 1063 3.85 C12 9 1065 3.84 3.58 3.86 3.43 3.81 C04C17 C16 C17 C16 10 1030 11 1037 12 1118 3.64 3.74 C27 Cl1 13 1007 3.583.81 3.83 3.59 C16 C15 C17 C16 14 Melagatran 3.67 999 C4  15 1090 3.763.82 3.63 C6  C5  C8  16 1089 17 1021 18 1097 3.61 3.8  3.78 3.84 3.62C8  N2  C9  C10 C11 19 54 20 1042 3.79 3.69 3.65 3.55 C26 C27 C26 C27 212018 22 1031 23 1153 24 1025 3.64 C17 25 1012 3.88 3.79 C5  C7  26 10783.66 3.84 3.68 3.78 C11 C12 C11 C12 27 1145 28 1050 3.68 C19 29 12533.73 C20 30 1257 3.8  C25 31 1297 3.66 3.54 3.89 3.67 C4  C9  C15 C9  321304 3.83 3.65 3.69 3.73 3.86 C7  C10 C11 C10 C11 33 1306 3.5  3.58 C11C12 34 1307 3.83 3.81 3.88 C7  C11 C12 35 1328 3.78 3.64 3.78 3.72 3.873.55 C7  C10 C11 C10 C11 Cl1 36 1334 3.78 3.7  3.6  3.6  C7  C10 C10 C1137 1335 3.82 C17 38 1338 3.79 3.88 3.88 3.9  3.63 3.6  C11 C12 C11 C15C16 C17 39 1345 40 1351 3.71 3.86 3.79 3.75 3.86 3.63 3.58 3.79 3.85 C7 C10 C11 C14 C15 C14 C15 C16 C17 41 1353 3.81 3.89 3.86 3.89 C4  C7  C10C11 42 1367 3.69 3.79 3.88 N5  C18 C19 43 1368 3.36 3.72 C09 C16 44 13713.74 3.74 3.8  3.42 3.87 3.8  C5  C7  C11 C12 C13 C12 45 1372 3.81 3.8 3.53 3.76 3.71 C16 C19 C20 C21 C20 46 1373 3.66 3.76 3.86 3.82 C10 C11C9  C10 47 1492 48 1399 3.84 3.82 3.84 3.77 3.78 3.61 C5  C10 C8  C10C14 C15 49 1406 3.86 3.6  C8  C24 50 1433 3.73 C15 51 14 52 1360 3.883.88 3.87 3.43 3.37 3.47 3.83 C18 C7  C14 C15 C14 C15 C12 53 1450 3.543.38 3.7  3.69 3.6  C12 C4  C6  C4  C5  54 1435 3.73 3.65 C7  C11 551441 3.59 3.66 3.72 3.85 3.78 C9  C15 C16 C15 C16 56 1411 3.6  3.81 3.563.62 3.25 C8  C12 C13 C12 C13 57 1149 3.58 3.71 3.89 C30 C31 C32 TABLEA2-6: van der Waals Amino Acid SER ASP SER MASP-2 AA# 611 627 628 AAatom CB OG CG OD1 OD2 C CA 1 1129 3.07 3.88 N19 C14 2 1034 3.18 3.75 N20C16 3 1024 3.54 3.04 3.62 C8  N4  C20 4 1059 3.36 3.34 3.87 3.44 N4  C22C19 C18 5 1088 3.54 3.83 3.84 3.76 3.66 3.81 N31 N29 C30 C30 N31 C30 61036 3.4  3.89 N27 C25 7 1081 3.86 3.19 C14 N27 8 1063 3.09 3.89 3.85N4  C23 N4  9 1065 3.54 3.79 3.76 3.84 3.85 3.8  3.8  3.85 C18 N29 N28C27 C27 N29 C27 C23 10 1030 3.11 3.62 3.74 N5  C21 N5  11 1037 3.31 3.683.8  N19 C17 C13 12 1118 3.73 3.15 3.79 Cl2 N5  C21 13 1007 3.57 3.883.36 3.82 C15 N5  N1  C2  14 Melagatran 3.02 3.61 3.85 3.69 999 N24 C23N24 C21 15 1090 3.33 3.51 3.09 3.45 3.75 3.54 N4  C23 C23 C23 C22 C24 161089 3.56 3.22 2.93 3.62 3.51 3.54 3.54 C22 N4  C22 C22 C23 C21 C22 171021 3.83 3.78 3.77 C2  C1  C2  18 1097 3.17 3.78 N5  C22 19 54 3.283.35 3.37 3.76 3.64 3.77 3.36 3.28 3.9  C12 C12 C12 C08 C12 C14 N10 N11N11 20 1042 3.62 3.64 3.64 3.84 C25 C26 N22 N22 21 2018 3.03 3.63 N5 C25 22 1031 3.89 3.65 3.83 3.5  3.48 C16 C23 C23 C22 C23 23 1153 3.872.95 3.72 3.54 3.32 C8  N2  C8  C8  N2  24 1025 3.84 3.41 N09 N05 251012 3.6  N4  26 1078 3.36 3.65 3.62 3.82 3.82 3.81 C12 C13 C20 C20 C19C20 27 1145 3.54 3.78 3.04 3.67 3.75 C10 C11 N4  C30 N4  28 1050 3.173.89 3.8  N3  C10 N3  29 1253 3.8  3.71 C25 N01 30 1257 3.75 3.82 C28N01 31 1297 3.78 3.28 3.33 3.57 C8  C8  C9  N4  32 1304 3.79 3.74 3.383.73 C12 C11 C12 N4  33 1306 3.84 3.47 3.01 3.49 3.38 C10 C10 N4  C23N4  34 1307 3.83 3.27 3.63 3.72 3.75 3.88 C10 C10 C11 C20 C23 C19 351328 3.83 3.57 3.61 C12 C22 N4  36 1334 3.89 3.73 3.18 3.82 3.76 3.81C12 N23 C23 C23 C23 N5  37 1335 3.09 3.71 3.8  N5  C23 N5  38 1338 3.463.78 3.69 3.68 C10 C11 C17 N4  39 1345 3.89 3.88 2.7 3.37 3.69 C21 C31N5  C31 N5  40 1351 3.79 3.73 C15 N4  41 1353 3.61 3.43 3.76 C8  C9  N4 42 1367 3.71 N3  43 1368 3.88 3.37 3.73 C26 C26 N34 44 1371 3.72 3.49C11 C20 45 1372 3.68 3.35 3.4  3.72 C18 C18 C19 N3  46 1373 3.63 3.393.88 3.73 C12 C7  S1  N4  47 1492 3.24 3.45 3.45 3.44 3.75 3.53 N6  C19C20 C23 C18 C19 48 1399 3.85 3.71 C7  N4  49 1406 3.78 3.68 3.11 3.663.79 C11 C10 C11 C12 N4  50 1433 3.7  3.14 3.79 3.7  3.74 C6  C6  C6 C6  N2  51 14 52 1360 3.68 C11 C12 C13 3.73 C12 3.74 3.63 3.82 N4  531450 3.51 3.57 3.82 2.86 3.84 3.61 2.89 3.79 3.63 3.53 C22 C24 N5  C22C24 C22 C24 C20 C22 N5  54 1435 3.78 3.77 Cl2 N4  55 1441 3.87 3.5  3.713.72 C14 C14 C15 N4  56 1411 3.73 3.66 3.38 3.82 3.77 C14 C13 C14 C22N4  57 1149 3.78 3.67 3.38 3.54 C32 N1  C8  C1  TABLE A2-7: van derWaals Amino Acid SER MASP-2 AA# 628 AA atom CB O OG 1 1129 3.47 3.463.34 3.71 C18 C15 C14 C14 2 1034 3.29 3.13 3.22 3.82 C18 C16 C15 C16 31024 3.34 3.43 3.42 3.66 C20 C18 C17 C18 4 1059 3.35 3.37 3.4  C19 C18C18 5 1088 3.11 3.81 C30 C24 6 1036 3.35 3.24 3.25 C25 C22 C21 7 10813.37 3.42 3.42 C25 C22 C21 8 1063 3.57 3.82 3.64 C23 C20 C21 9 1065 2.893.46 3.66 3.59 C27 C24 C23 C23 10 1030 3.43 3.79 3.38 C21 C18 C19 111037 3.34 3.1  2.92 C17 C14 C13 12 1118 3.34 3.1  2.92 3.57 3.26 C17 C14C13 C12 C17 13 1007 3.13 3.44 C3  C2  14 Melagatran 3.87 3.06 3.27 3.1 3.89 3.63 999 C20 C23 C21 C20 C19 C21 15 1090 3.64 3.77 3.77 2.93 3.213.18 3.46 C23 C15 C22 C23 C24 C24 C23 16 1089 3.79 3.32 2.97 C23 3.113.26 C19 C21 C22 3.48 C21 C22 17 1021 3.79 3.05 3.05 3.78 C6  C1  C2 C3  18 1097 3.39 3.46 3.54 3.71 C18 C19 C22 C18 19 54 3.86 3.58 3.612.56 2.88 3.38 3.78 N11 O09 C08 C12 C14 C08 C12 20 1042 3.55 3.58 3.26C16 C17 C20 21 2018 3.48 3.33 3.36 3.77 3.14 C21 C22 C25 C20 C21 22 10313.64 3.62 3.18 3.28 C23 C24 C22 C23 23 1153 3.7  3.16 3.35 C2  C8  C3 24 1025 3.3  3.06 C04 C06 25 1012 3.53 C17 26 1078 3.85 3.07 3.1  3.893.86 3.34 3.86 C18 C19 C20 C21 C20 C21 C22 27 1145 3.59 3.27 3.36 C27C30 C28 28 1050 3.34 3.58 3.39 C10 C7  C6  29 1253 3.58 C02 30 1257 3.683.84 3.85 C02 C06 C07 31 1297 3.79 3.51 3.61 C22 C23 C26 32 1304 3.65C19 33 1306 3.65 3.63 3.33 3.89 3.51 C19 C20 C23 C18 C19 34 1307 3.673.76 3.45 3.63 3.4  C21 Cl1 C19 C20 C23 35 1328 3.67 3.76 3.76 3.79 3.51C22 C18 C19 C22 C22 36 1334 3.83 3.73 3.25 Cl1 C19 C23 37 1335 3.65 3.423.28 C1  C23 C2  38 1338 3.81 3.52 C22 C23 39 1345 3.66 3.33 3.12 3.33C27 C28 C31 C27 40 1351 3.89 3.7  C28 C25 41 1353 3.66 C19 42 1367 3.56C8  43 1368 3.63 C35 44 1371 3.87 3.41 3.36 3.75 3.15 3.78 Cl1 C19 C20C20 C21 C22 45 1372 3.68 C9  46 1373 3.64 C19 47 1492 3.82 3.81 3.243.38 3.16 2.8  C19 C18 C19 C20 C18 C19 48 1399 3.61 C22 49 1406 3.76 C2050 1433 3.67 3.64 3.71 3.22 3.89 C7 Cl1 C5 C6 C7 51 14 3.65 C14 52 1360C24 3.61 53 1450 3.65 3.71 C19 C20 C22 C23 C24 C23 Cl1 3.88 3.33 3.013.71 2.95 54 1435 C19 3.67 55 1441 3.85 3.53 C19 C20 56 1411 3.82 3.76C22 C20 57 1149 3.41 3.69 3.44 C1  C2  C8  Amino Acid CYS MASP-2 AA# 629AA atom CA 1 1129 3.75 3.66 C17 C12 2 1034 3.89 3.69 3.48 3.69 3.86 3.893.85 3.83 C17 C13 C12 C11 C17 C14 C13 C12 3 1024 3.75 3.75 C15 C14 41059 3.72 3.76 3.86 C17 C16 C17 5 1088 6 1036 3.49 3.75 3.82 3.82 C24C19 C24 C23 7 1081 3.8  C19 8 1063 9 1065 3.78 3.76 C22 C21 10 1030 111037 3.61 3.56 3.85 C16 C11 C10 12 1118 3.76 3.89 C20 C15 13 1007 3.8 3.8  3.53 3.41 3.76 3.55 3.61 C19 C5  C2  C1  C3  N1  C2  14 Melagatran3.68 3.64 3.8 3.84 3.88 3.74 3.55 3.48 3.67 999 C18 C17 C16 C22 C21 C20C19 C18 C17 15 1090 3.89 C15 16 1089 17 1021 3.84 3.58 C1  C6  18 109719 54 3.88 3.73 3.79 3.74 C08 C14 N10 N15 20 1042 21 2018 3.87 C24 221031 3.76 3.62 3.67 C21 C22 O26 23 1153 3.85 C2  24 1025 3.83 3.84 3.48C04 C06 N05 25 1012 3.71 3.72 C16 N4  26 1078 3.74 3.63 C18 O3  27 11453.85 C26 28 1050 29 1253 3.75 3.68 C06 N01 30 1257 3.86 3.86 C06 N01 311297 3.6  3.89 3.55 C22 C23 N4  32 1304 3.81 N4  33 1306 34 1307 3.8 3.7  C18 O3  35 1328 3.59 3.86 3.6  C18 C22 N4  36 1334 3.77 3.66 C19N4  37 1335 3.84 C6  38 1338 3.75 3.74 C22 N4  39 1345 3.62 3.71 C29 C3040 1351 3.85 3.82 C24 N4  41 1353 3.76 3.65 C18 N4  42 1367 3.89 3.79C7  N3  43 1368 3.86 3.76 C33 N4  44 1371 3.76 N5  45 1372 3.9  3.78 C6 N3  46 1373 3.83 N4  47 1492 3.86 C17 48 1399 3.81 N4  49 1406 3.81 3.78C19 N4  50 1433 3.77 3.66 C5  N1  51 14 3.89 C14 52 1360 3.86 3.75 C23N4  53 1450 3.78 3.57 C20 N4  54 1435 3.88 3.85 C18 N4  55 1441 3.873.83 C19 N4  56 1411 3.68 3.72 C21 N4  57 1149 3.68 3.82 C1  C6  TABLEA2-8: van der Waals Amino Acid CYS ARG MASP-2 AA# 629 630 AA atom CB N CO CA CB CD 1 1129 3.88 3.66 3.6  3.67 C13 C12 C11 O25 2 1034 3.74 3.6 3.8  C12 C11 C11 3 1024 4 1059 3.65 3.83 3.73 3.8  C18 C17 C17 O1 5 10886 1036 3.84 3.66 3.58 C24 C19 C18 7 1081 3.8  3.86 C19 C18 8 1063 9 10653.65 3.82 C22 C21 10 1030 11 1037 3.8  3.44 3.38 3.86 C12 C11 C10 C10 121118 13 1007 3.41 3.4  3.39 C19 C2 C1 14 Melagatran 3.84 3.76 3.86 999C19 C16 O31 15 1090 3.9 C16 16 1089 17 1021 3.78 3.52 3.8  3.66 3.863.47 C5  C6  C7  C5  C6  C7  18 1097 3.83 3.88 3.81 3.89 C16 C21 C15 C1619 54 3.71 3.62 3.77 3.79 3.68 3.86 C01 C02 C02 C05 C06 C06 20 1042 3.683.76 3.54 3.27 3.2  3.82 C14 C15 C13 C14 C15 C16 21 2018 3.78 3.6  3.583.64 3.81 3.39 C18 C19 C24 C18 C19 O3  22 1031 3.72 3.84 3.53 2.94 C22C21 O26 O04 23 1153 3.85 3.8  3.8  3.52 3.43 2.94 C3  C4  C7  C9  N3 O1  24 1025 3.53 3.74 3.69 3.17 C04 N05 C03 C04 25 1012 3.88 3.55 3.7 3.72 3.73 3.83 C16 C15 C16 C14 C15 C16 26 1078 3.86 3.51 C18 O3  27 11453.84 3.69 3.83 3.43 3.49 3.62 C24 C25 C24 C15 C16 C17 28 1050 3.78 3.88C9  C4  29 1253 3.62 3.66 3.85 3.82 3.73 3.82 3.86 C05 C06 C05 C06 C08C09 C09 30 1257 3.68 3.73 3.8  3.89 C05 C06 C07 C09 31 1297 3.87 3.583.54 3.89 3.79 3.81 3.69 3.57 C26 C21 C22 C26 C20 C21 C22 C26 32 13043.71 3.75 3.9  3.85 3.71 3.89 C17 C18 C16 C18 C22 C16 33 1306 34 13073.77 3.48 3.54 3.87 C18 O3 C16 C17 35 1328 3.81 3.55 3.74 3.68 3.85 3.853.68 C18 C22 C17 C18 C16 C18 C22 36 1334 3.71 3.78 C18 N4  37 1335 3.823.7  3.86 C4  C5  C4  38 1338 3.9  3.61 3.71 3.71 3.76 3.76 3.75 C20 C21C22 C20 C21 C22 C26 39 1345 3.89 3.55 3.85 3.37 3.45 3.37 3.77 3.68 3.72C24 C25 C29 C30 C24 C25 C26 C30 O1  40 1351 3.62 3.73 3.85 3.85 3.833.73 3.86 C23 C24 C22 C23 C24 C28 C22 41 1353 3.72 3.68 3.85 3.87 3.753.69 C17 C18 C16 C17 C18 C22 42 1367 3.74 3.78 3.78 C6  C7  C11 43 13683.66 3.69 3.85 3.8  3.74 C32 C33 C32 C33 C39 44 1371 3.52 3.75 3.83 N5 N5  N6  45 1372 3.73 3.72 3.69 3.83 C5  C6  C22 C6  46 1373 3.68 3.773.87 3.86 3.72 C17 C18 C17 C18 C22 47 1492 3.8  3.51 3.66 3.5  C18 C16C17 C16 48 1399 3.69 3.73 3.84 3.73 C20 C21 C21 C25 49 1406 3.69 3.743.87 3.87 3.71 C18 C19 C17 C19 C23 50 1433 3.88 3.55 3.61 3.77 3.89 C3 C4  N1  C3  C4  51 14 3.83 3.58 3.51 3.63 3.78 C13 C14 C13 C14 C1  521360 3.68 3.77 3.81 3.82 3.83 3.75 C22 C23 C21 C22 C23 C27 53 1450 3.863.51 3.62 3.77 3.88 C17 C21 N4  C17 C21 54 1435 3.71 3.78 3.84 C17 C18C22 55 1441 3.6  3.75 3.85 3.89 3.82 3.83 3.85 C1  C19 C1  C19 C2 C23C2  56 1411 3.72 3.81 3.59 3.67 3.89 3.62 3.76 3.74 3.51 3.85 3.47 3.72C22 C16 C17 C21 C22 C16 C17 C21 C22 C16 O3  O4  57 1149 3.64 3.66 3.54C1  C6  C6  TABLE A2-9 van der Waals Amino Acid ARG MASP-2 AA# 630 AAatom CG CZ 1 1129 3.41 3.85 O25 O08 2 1034 3 1024 4 1059 3.14 O1  5 10883.79 O03 6 1036 7 1081 3.76 O11 8 1063 9 1065 3.55 O13 10 1030 11 103712 1118 3.85 O2  13 1007 3.61 O1  14 Melagatran 3.8  999 O31 15 10903.64 O1 16 1089 17 1021 18 1097 19 54 3.89 3.31 2.93 C01 C05 C06 20 104221 2018 22 1031 3.05 3.17 3.86 O04 O04 O09 23 1153 3.89 3.51 3.86 3.253.76 3.78 3.87 3.03 C6  C7  C9  N3  O1  C7  C9  O1  24 1025 25 1012 3.83O1  26 1078 3.78 O2  27 1145 3.44 3.77 3.6  2.85 3.57 C15 C15 C16 C17C18 28 1050 3.66 O1  29 1253 3.77 3.63 C04 O13 30 1257 3.53 O13 31 12973.47 O2  32 1304 3.71 3.7  C21 O2  33 1306 34 1307 3.57 3.85 O2  O3  351328 3.9  3.79 C21 O2  36 1334 3.89 C18 37 1335 3.48 O3  38 1338 3.75O2  39 1345 3.52 O1  40 1351 3.81 C27 41 1353 3.74 C21 42 1367 3.86 O1 43 1368 3.67 3.78 C37 O30 44 1371 45 1372 3.68 3.69 C7  O1  46 1373 3.7 3.66 C21 O2  47 1492 48 1399 3.73 3.74 C24 O1  49 1406 50 1433 51 143.73 3.71 3.8  C10 C11 N1  52 1360 53 1450 54 1435 55 1441 3.87 O2  561411 3.7  3.57 3.71 C18 O3  O3  57 1149 Amino Acid ARG MASP-2 AA# 630 AAatom N NE NH1 1 1129 3.69 C17 2 1034 3.45 3.63 3.71 C13 C12 C11 3 10243.48 3.83 C15 C14 4 1059 5 1088 3.9  3.83 C26 C27 6 1036 3.5  C24 7 10813.81 C24 8 1063 3.71 3.88 C18 C17 9 1065 3.77 3.82 C26 C21 10 1030 3.83C16 11 1037 3.54 3.86 C16 C11 12 1118 3.67 C20 13 1007 3.77 3.74 C5  C1 14 Melagatran 3.64 3.89 999 C18 C16 15 1090 3.85 C11 16 1089 3.88 3.86C15 C16 17 1021 3.89 C6  18 1097 3.71 C21 19 54 3.5 3.86 3.63 C01 C02C06 20 1042 21 2018 3.89 3.82 3.43 3.28 3.34 3.33 C18 C19 C24 C1  C2 C26 22 1031 3.34 3.81 C03 C08 23 1153 3.86 C6  24 1025 25 1012 3.74 3.73C15 C19 26 1078 27 1145 3.58 3.69 3.37 2.93 3.51 3.72 3.55 C25 C15 C16C17 C18 C15 C17 28 1050 3.66 C9  29 1253 3.78 3.69 C04 C05 30 1257 3.813.72 C04 C05 31 1297 3.87 3.61 3.76 C20 C21 C25 32 1304 3.76 3.88 C17C21 33 1306 3.76 C22 34 1307 35 1328 36 1334 3.59 C18 37 1335 3.57 C5 38 1338 3.88 3.7  3.71 C20 C21 C25 39 1345 3.44 3.31 C30 C14 40 13513.89 3.69 3.76 C22 C23 C27 41 1353 3.81 3.89 C17 C21 42 1367 3.8  C6  431368 3.71 3.81 C32 C37 44 1371 3.44 N5  45 1372 3.79 3.86 C5  C7  461373 3.76 3.86 C17 C21 47 1492 3.71 C16 48 1399 3.75 3.81 3.82 C20 C24C23 49 1406 3.7  3.81 C18 C22 50 1433 3.49 C4  51 14 52 1360 53 1450 541435 55 1441 3.68 3.89 3.72 C1  C2  C22 56 1411 3.88 3.76 3.87 C16 C17C18 57 1149 TABLE A2-10 van der Waals Amino Acid ARG ASP SER MASP-2 AA#630 GLY 632 633 AA atom NH2 631 C CA CB O OG O 1 1129 3.11 3.9  C11 C062 1034 3.11 C11 3 1024 3.41 C13 4 1059 3.51 C15 5 1088 3.7  C20 6 10363.53 3.8  C18 C15 7 1081 3.36 C18 8 1063 3.67 C16 9 1065 3.14 C20 101030 3.31 C14 11 1037 3.31 C10 12 1118 3.4  C14 13 1007 3.2  C19 14Melagatran 2.98 999 C16 15 1090 3.2  3.61 C21 C21 16 1089 3.17 C14 171021 3.29 3.8 C7  C8  18 1097 3.45 C15 19 54 2.86 2.68 C03 C04 20 10423.28 C13 21 2018 3.17 C18 22 1031 3.7  C01 23 1153 3.36 3.32 C9  C7  241025 3.82 C02 25 1012 3.47 C14 26 1078 3.71 3.75 3.75 3.85 3.5  C1  C15C2  C3  C16 27 1145 2.92 3.23 3.23 C17 C18 C23 28 1050 3.17 C3  29 12533.82 3.22 C03 C09 30 1257 3.24 C09 31 1297 3.19 C20 32 1304 3.29 C16 331306 3.39 C16 34 1307 3.18 C16 35 1328 3.14 C16 36 1334 3.35 C16 37 13353.44 C7  38 1338 3.47 C20 39 1345 3.31 C24 40 1351 3.53 C22 41 1353 3.31C26 42 1367 3.37 C5  43 1368 3.75 3.32 C36 C31 44 1371 3.68 C16 45 13723.88 3.3  C8  C4  46 1373 3.27 C16 47 1492 3.49 C16 48 1399 3.31 C19 491406 3.25 C17 50 1433 3.17 C8  51 14 3.25 3.61 2.34 3.08 3.89 3.14 3.692.4 3.37 2.66 3.09 N3  C15 C16 C17 O3  O7  C16 N3  N3  C16 C17 52 136053 1450 54 1435 55 1441 3.88 3.38 C21 C2  56 1411 3.62 3.47 C25 C16 571149 3.45 C7  TABLE A2-11 van der Waals Amino Acid GLY GLY MASP-2 AA#634 635 AA atom C CA N N 1 1129 2 1034 3 1024 4 1059 5 1088 6 1036 71081 8 1063 9 1065 10 1030 11 1037 12 1118 13 1007 14 Melagatran999 151090 16 1089 17 1021 18 1097 19 54 20 1042 21 2018 22 1031 23 1153 241025 25 1012 26 1078 27 1145 28 1050 29 1253 30 1257 31 1297 32 1304 331306 34 1307 35 1328 36 1334 37 1335 38 1338 39 1345 40 1351 41 1353 421367 43 1368 44 1371 45 1372 46 1373 47 1492 48 1399 49 1406 50 1433 5114 3.52 3.74 3.81 2.57 3 3.12 2.33 3.52 C17 O7 C16 C17 O7 C15 C16 C17 521360 53 1450 54 1435 55 1441 56 1411 57 1149 Amino Acid VAL SER MASP-2AA# 653 654 AA atom CB CG1 O C 1 1129 3.9  3.65 3.8  3.74 3.71 C13 N10C11 C06 C01 2 1034 3.83 C11 3 1024 3.75 3.72 3.7  3.62 N3  C13 C12 C11 41059 3.81 3.87 3.73 C17 N1  C15 5 1088 3.62 3.55 3.68 3.55 3.74 3.5 C23C22 C22 C22 C21 C20 6 1036 3.52 3.52 3.75 3.71 N17 C18 C15 C14 7 10813.84 3.78 3.74 3.72 3.71 C20 N17 C18 C10 C09 8 1063 3.87 3.76 3.65 C16C9 C8 9 1065 3.6  3.78 C22 C20 10 1030 3.79 3.62 3.77 3.81 N3  C14 C13C12 11 1037 3.9  3.79 3.85 C12 C10 C06 12 1118 3.86 3.84 3.79 3.76 3.733.7  C16 N09 N3  C14 C7  C6  13 1007 3.76 3.85 3.85 C19 C7  C6  14Melagatran999 3.66 C16 15 1090 16 1089 17 1021 3.43 3.84 C4  C4  18 10973.73 N4  19 54 3.75 O09 20 1042 3.36 O11 21 2018 3.79 N3  22 1031 3.583.77 3.56 C25 C01 C25 23 1153 3.9  C4  24 1025 25 1012 26 1078 3.49 3.663.48 C22 C22 N1  27 1145 3.9  C29 28 1050 3.74 C5  29 1253 3.31 C08 301257 3.36 C07 31 1297 3.22 C26 32 1304 3.27 C22 33 1306 34 1307 3.473.79 C22 N1  35 1328 3.23 3.62 C22 C16 36 1334 3.55 3.81 3.72 3.79 C21Cl1 C22 N3  37 1335 3.83 3.71 C3  N3  38 1338 3.33 3.89 3.76 C26 C21 N3 39 1345 3.84 N1  40 1351 3.3  C28 41 1353 3.3  C22 42 1367 3.35 C11 431368 3.32 C39 44 1371 3.43 3.87 3.9  C22 Cl1 C26 45 1372 3.32 C22 461373 3.34 C22 47 1492 3.61 3.88 C18 N1  48 1399 3.32 3.89 3.62 C25 C22N3  49 1406 3.27 3.59 C23 N4  50 1433 3.71 3.88 3.89 C2  C2  N3  51 143.77 3.71 3.44 3.77 3.45 3.71 3.57 3.67 C16 C13 C16 N3 O3  C15 C16 C1752 1360 53 1450 3.81 C18 54 1435 55 1441 3.38 C23 56 1411 3.52 C22 571149 3.68 N3  TABLE A2-12: van der Waals Amino Acid SER TRP MASP-2 AA#654 655 AA atom O C CA 1 1129 3.64 3.75 3.56 3.7  3.25 C14 C13 O07 N10O07 2 1034 3.88 3.71 3.64 3.42 C17 C16 O07 O07 3 1024 3.71 3.66 3.5 3.28 3.66 3.76 O2  C19 C18 O2  C19 N3  4 1059 3.85 3.76 3.82 3.49 3.61C21 C20 O2  O2  N1  5 1088 3.62 3.72 3.89 3.82 3.76 3.47 3.89 C24 C23O07 C23 C22 O07 N01 6 1036 3.84 3.19 3.21 3.83 3.4  3.33 3.63 3.85 C22C21 C20 C19 O29 C20 C19 C18 7 1081 3.83 3.49 3.84 3.88 3.67 3.5  C22 C21C20 C21 C20 O05 8 1063 3.75 3.48 3.77 3.62 3.22 3.89 C22 C21 O1  C22 O1 C7  9 1065 3.61 3.73 3.89 3.46 C24 C23 O09 O09 10 1030 3.77 3.57 3.443.4  3.6  3.68 O2  C20 C19 O2  C20 N3  11 1037 3.5  3.68 3.8  3.85 3.3 C13 C12 O04 C12 O04 12 1118 3.34 3.57 3.73 3.61 3.78 3.32 C17 C16 O1 C16 N3  O1  13 1007 3.31 O2  14 Melagatran999 3.73 3.57 3.89 3.79 3.85C22 C21 C20 C22 O14 15 1090 3.79 3.65 3.87 3.59 3.88 3.83 C14 C15 C16O2  N2  C16 16 1089 3.57 3.82 3.61 3.77 3.55 3.76 3.84 3.84 C14 C20 C19C18 O2  C20 C15 N3  17 1021 3.73 3.83 3.84 3.9  3.82 3.74 3.72 3.38 3.573.38 3.68 3.87 C9  C8  C7  C4  C11 O1  C4  C3  C2  O1  C4  C3  18 10973.76 3.75 3.59 3.67 3.59 3.76 3.79 3.8  3.34 C13 C14 C15 C17 C18 O2  N4 C17 O2  19 54 3.69 3.58 3.81 3.57 3.41 3.61 C03 C04 C02 C08 O09 C03 201042 3.84 3.85 3.17 3.57 3.67 3.78 3.89 3.23 C10 C13 C15 C16 C15 C16 O05O11 21 2018 3.46 3.68 3.88 3.53 3.48 3.88 3.73 3.74 3.45 C16 C17 C18 C20C21 O2  C20 N3  O2  22 1031 3    3.17 3.76 3.59 3.67 3.4  3.26 3.64 3.523.25 3.68 C01 C07 C20 C25 C20 C24 C25 C01 C20 C25 N06 23 1153 3.77 3.763.86 3.58 3.19 C10 C7  C3  O2  O2  24 1025 3.51 3.68 C02 O26 25 10123.68 3.76 3.87 3.8  3.36 C12 C13 C14 O2  O2  26 1078 3.59 3.48 3.62 3.673.39 3.5  3.87 3.71 3.88 3.42 3.48 3.55 C1  C16 C2  C20 C21 C22 O1  C17C21 C22 N1  O1  27 1145 3.81 3.89 3.61 3.45 3.57 3.71 3.59 3.74 3.28 C1 C2  C23 C28 C29 O2  C29 N1  O2  28 1050 3.72 3.47 3.31 3.74 3.85 3.773.48 3.89 3.66 3.47 C3  C5  C6  C7  O2  C4  C5 C6 N2 O2 29 1253 3.823.83 3.8  3.82 3.41 C09 C12 N01 O17 O17 30 1257 3.73 3.86 3.76 3.57 C09C06 N01 O37 31 1297 3.51 3.89 3.49 C20 N4  O1  32 1304 3.87 3.88 3.793.82 3.76 3.83 3.42 C1  C15 C16 C18 N4  O1  O1  33 1306 3.71 3.08 3.583.72 3.71 3.69 3.68 3.67 3.35 C1  C16 C18 C19 O1  C16 C17 C18 O1  341307 3.74 3.79 3.73 3.56 3.4  3.61 3.64 3.84 3.59 3.79 3.3  C1  C15 C16C20 C21 C22 O1  C17 C22 N3  O1  35 1328 3.79 3.65 3.44 3.73 3.45 C1  C15C16 N3  O1  36 1334 3.82 3.77 3.58 3.51 3.74 3.69 3.81 3.6  3.88 3.42C1  C15 C16 C20 C21 C22 O1  C21 N3  O1  37 1335 3.79 3.9  3.87 3.48 3.683.73 3.73 3.87 3.36 C7  C8  C9  C2  C3  O1  C3  N1  O1  38 1338 3.863.88 3.81 3.84 3.82 3.84 3.4  C1  C19 C20 C26 N4  O1  O1  39 1345 3.753.61 3.61 3.66 3.81 3.7  3.25 C24 C26 C27 O2  C26 N1 O2  40 1351 3.893.9  3.81 3.86 3.8  3.81 3.34 C1  C21 C22 C28 N4  O1  O1  41 1353 3.863.89 3.82 3.8  3.72 3.3  C14 C15 C16 N4  O1  O1  42 1367 3.87 3.81 3.733.29 C5  N3  O2  O2  43 1368 3.85 3.89 3.71 3.29 C03 N34 O29 O29 44 13713.53 3.66 3.85 3.89 3.63 3.56 3.83 3.81 3.72 3.69 3.4 C1  C15 C16 C19C20 C21 C22 O1  C22 N3  O1  45 1372 3.9  3.89 3.77 3.85 3.88 3.48 C1 C3  C4 N3  O2  O2  46 1373 3.83 3.84 3.77 3.84 3.44 C16 C18 N4  O1  O1 47 1492 3.25 3.47 3.82 3.7  3.87 3.58 3.33 C14 C15 C16 O1  C15 N4  O1 48 1399 3.88 3.85 3.83 3.75 3.84 3.43 C17 C19 C21 N4  O2  O2  49 14063.88 3.76 3.88 3.81 3.72 3.87 3.84 3.89 3.38 C16 C17 C2  C19 N4  O1  C19N3  O1  50 1433 3.89 3.89 3.57 3.87 3.5  3.74 3.67 3.75 3.62 3.37 C10C2  C8  C9  C1  C2  C7  O2  C2  O2  51 14 3.54 3.21 3.72 3.69 C12 C8 C9  O1  52 1360 3.89 3.85 3.9  3.85 3.82 3.44 C1  C21 C23 N4  O1  O1  531450 3.68 3.79 3.65 3.39 3.54 3.67 3.53 3.85 3.9  3.31 C16 C18 C18 C19C23 O1  C18 C19  N3  O1  54 1435 3.88 3.9  3.85 3.87 3.75 3.87 3.41 C1 C15 C16 C18 N4  O1  O1  55 1441 C4  3.88 3.77 3.77 3.34 3.85 C19 N4  O1 O1  56 1411 C1  C3  3.86 3.61 3.14 3.77 3.88 N4  O2  O2  57 1149 C7  C9 3.82 3.83 3.87 3.88 3.73 3.51 3.61 3.34 3.69 C1  C2  C3  C6  C5  N3  O2 Amino Acid TRP MASP-2 AA# 655 AA atom CB CD CE2 1 1129 3.26 O07 2 10343.4  3.87 O07 C05 3 1024 3.23 3.89 3.84 O2  C1  C6  4 1059 3.3  O2  51088 3.34 O07 6 1036 3.22 O29 7 1081 3.31 3.48 O05 C16 8 1063 3.25 3.423.65 3.84 O1  C7  C2  C1  9 1065 3.35 O09 10 1030 3.24 O2  11 1037 3.2 3.69 O04 C01 12 1118 3.68 C13 13 1007 3.13 3.89 O2  C9  14 Melagatran99915 1090 3.31 O2  16 1089 3.39 O2  17 1021 3.59 O1  18 1097 3.27 O2  1954 20 1042 3.64 3.33 O05 O11 21 2018 3.15 O2  22 1031 3.53 N06 23 11533.87 3.05 C12 O2  24 1025 3.84 O26 25 1012 3.89 3.32 C11 O2  26 10783.52 O1  27 1145 3.88 3.08 3.67 C3  O2  C12 28 1050 3.23 3.9  O2  C17 291253 3.31 O17 30 1257 3.36 O17 31 1297 3.38 O1  32 1304 3.89 3.3  C2 O1  33 1306 3.33 O1  34 1307 3.33 O1  35 1328 3.4  O1  36 1334 3.31 O1 37 1335 3.38 3.84 O1  C15 38 1338 3.9  3.32 C2  O1  39 1345 3.23 O2  401351 3.8  3.24 C2  O1  41 1353 3.77 3.22 C13 O1  42 1367 3.71 3.22 C2 O2  43 1368 3.81 3.27 3.52 C06 O29 C28 44 1371 3.45 O1  45 1372 3.35 O2 46 1373 3.87 3.34 C2  O1  47 1492 3.44 O1  48 1399 3.85 3.31 3.76 C16O2  S1  49 1406 3.84 3.13 C3  O1  50 1433 3.32 O2  51 14 3.68 O1  521360 3.36 O1  53 1450 3.83 3.28 C1  O1  54 1435 3.3  O1  55 1441 3.8 3.25 C5  O1  56 1411 3.63 3.02 C4  O2  57 1149 3.88 3.24 C12 O2  TABLEA2-13: van der Waals Amino Acid TRP MASP-2 AA# 655 AA atom CE3 CH2 CZ2CZ3 N O 1 1129 3.54 3.9  C14 C13 2 1034 3.77 C16 3 1024 3.9  3.5  3.863.86 3.78 3.59 C7  C6  C7  C6  C19 C18 4 1059 3.66 3.57 3.23 3.84 3.88C13 C9  C16 C13 C19 5 1088 3.78 3.7  3.77 3.72 3.75 C23 C22 C30 C24 C236 1036 3.58 3.2  3.48 C20 C21 C20 7 1081 3.23 3.86 3.9  3.67 3.82 3.833.8  C16 C15 C08 C16 C15 C20 C21 8 1063 3.83 3.81 3.84 C15 C2  C21 91065 3.6  C19 10 1030 3.81 3.8 3.39 C20 C20 C19 11 1037 3.25 3.64 C13C12 12 1118 3.4  3.8  3.66 3.87 3.69 3.76 3.4  3.88 C13 C5  C4  Cl2 C13C16 C17 C16 13 1007 3.69 3.78 C14 C14 14 Melagatran 3.75 3.79 3.39 999C6  C22 C21 15 1090 3.81 3.79 C15 C24 16 1089 3.59 3.77 3.71 C10 C21 C1917 1021 3.88 3.61 3.31 3.6  C3  C4  C3  C2  18 1097 3.87 3.56 C17 C18 1954 3.7  C08 20 1042 3.42 3.65 3.88 3.38 3.45 C24 C25 C25 C24 C25 21 20183.76 3.89 3.74 3.42 C11 C20 C20 C21 22 1031 3.49 3.68 3.28 3.31 3.54 C15C15 C25 C24 C25 23 1153 3.61 3.78 3.85 C17 C18 C3  24 1025 25 1012 261078 3.71 3.28 3.62 3.47 3.85 3.29 3.77 3.39 3.83 C13 C14 C13 C14 C23C22 C20 C21 C22 27 1145 3.49 3.79 3.47 3.84 C12 C29 C28 C29 28 1050 3.843.5  3.81 3.74 3.56 3.09 3.72 C15 C17 C17 C5 C5 C6 C7 29 1253 3.61 3.71C24 C24 30 1257 3.87 3.74 3.77 C23 C28 C28 31 1297 3.54 3.86 3.38 3.7C7  C8  C7  C8  32 1304 3.78 3.68 C13 C13  33 1306 3.87 3.44 3.84 3.663.27 3.85 3.78 3.79 3.75 C10 C9  C10 C10 C9  C16 C18 C18 C19 34 13073.75 3.76 3.87 3.48 3.57 3.3  3.85 C9  C9  C21 C22 C20 C21 C22 35 13283.49 3.53 C13 C13 36 1334 3.66 3.67 3.68 3.68 3.38 C13 C13 C21 C20 C2237 1335 3.84 3.39 3.7  3.82 3.44 3.9  C13 C15 C15 C3  C2  C3  38 13383.83 3.74 3.9  C9  C9  C26 39 1345 3.77 3.52 C26 C27 40 1351 41 1353 421367 3.89 3.86 C21 C21 43 1368 3.52 3.87 C28 C28 44 1371 3.78 3.63 3.7 3.68 3.86 3.54 3.56 3.42 C10 C9 C10 C9  C21 C22 C20 C21 45 1372 3.543.48 C17 C17 46 1373 3.65 3.57 C13 C13 47 1492 3.74 C12 48 1399 3.893.49 3.65 3.42 C3  S1  S1  S1  49 1406 3.7  3.84 3.51 3.85 C10 C10 C10C23 50 1433 3.59 3.73 3.68 3.75 3.44 C22 C22 C2  C1  C7  51 34 52 136053 1450 3.66 3.63 3.79 3.26 C18 C19 C22 C23 54 1435 55 1441 3.65 3.75C13 C13 56 1411 3.6  3.57 C15 C15 57 1149 3.6  3.85 3.88 C1  C2  C6 Amino Acid GLY MASP-2 AA# 656 AA atom C CA 1 1129 3.54 3.47 3.66 3.66N20 N20 C18 C15 2 1034 3.63 3.7  3.84 3.83 3.86 N19 O07 N19 C18 O07 31024 3.53 3.54 3.57 3.58 N5  N5  C20 C17 4 1059 3.28 3.83 3.4  3.69 3.85N5  C22 N5  C22 C20 5 1088 3.75 3.56 3.75 3.67 3.89 C28 N18 N29 C28 C276 1036 3.48 3.83 3.88 3.82 3.64 3.56 3.75 N26 C25 C22 N26 C25 C22 C21 71081 3.27 3.28 3.54 3.83 N26 N26 C25 C22 8 1063 3.36 3.24 3.46 3.64 N5 N5  C23 C20 9 1065 3.88 3.74 N28 C27 10 1030 3.73 3.86 N4  N4  11 10373.7  3.69 3.79 N18 C17 C14 12 1118 3.63 3.7  3.78 3.88 N4  N4  C21 C1813 1007 3.74 3.63 3.86 N5  N5  C3  14 Melagatran 3.42 3.42 3.59 3.69 999N25 N25 C23 C20 15 1090 3.82 3.86 3.44 3.74 3.5  3.37 3.44 C13 C22 N5 C13 C34 C22 N5  16 1089 3.84 3.59 3.83 3.66 3.67 3.67 C17 N5  C17 C18C23 N5  17 1021 3.76 3.72 3.55 N3  C1  C2  18 1097 3.46 3.81 3.78 3.65N6  C19 C22 N6  19 54 3.86 3.66 C14 N10 20 1042 3.86 3.57 3.45 3.29 3.853.85 3.53 3.76 3.76 C17 C20 N03 M21 O05 C17 C20 N21 N22 21 2018 3.643.82 3.85 3.81 N4  C22 C25 N4 22 1031 3.61 N11 23 1153 3.88 N1  24 10253.88 3.89 C18 N19 25 1012 3.86 3.53 3.73 3.57 C17 N5  C17 N5  26 10783.87 3.89 3.76 3.66 C5  O1  C19 C20 27 1145 3.78 3.54 3.82 3.79 3.61 N3 N5  C27 C30 N5  28 1050 3.54 3.6  3.7  3.77 3.46 N4  N5  C10 C7  N4  291253 3.85 3.52 3.67 3.52 C02 N07 C02 N07 30 1257 3.72 3.39 3.63 3.883.45 C02 N08 C02 N01 N08 31 1297 3.88 3.65 3.59 3.44 N1  N5  C23 N5  321304 3.82 3.56 3.61 3.49 C19 N5  C19 N5  33 1306 3.54 3.61 N5  N5  341307 3.7  3.64 3.78 C19 C20 C23 35 1328 3.67 3.31 3.53 3.76 3.41 C19 N5 C19 N4  N5  36 1334 3.78 3.85 3.58 C19 C23 N5  37 1335 3.51 3.86 3.6 N6  C23 N6  38 1338 3.86 3.56 3.75 3.57 C23 N5  C23 N5  39 1345 3.743.83 3.52 3.63 3.51 N6  C27 C28 C33 N6  40 1351 3.84 3.45 3.62 3.37 C25N5  C25 N5  41 1353 3.77 3.44 3.68 3.5  C19 N5  C19 N5  42 1367 3.8 3.49 3.78 3.61 C8  N4  C8  N4  43 1368 3.72 3.46 3.67 3.55 C35 N38 C35N38 44 1371 3.84 3.52 3.69 N2  C19 C20 45 1372 3.73 3.47 3.6  3.49 C9 N4  C9  N4  46 1373 3.82 3.52 3.68 3.53 C19 N5  C19 N5  47 1492 3.723.31 3.72 3.65 3.47 C23 N5  C21 C23 N5  48 1399 3.73 3.41 3.61 3.44 C22N5  C22 N5  49 1406 3.84 3.54 3.62 3.46 C20 N5  C20 N5  50 1433 3.883.67 C5  N2  51 34 3.72 C9  52 1360 3.8 3.47 3.68 3.5  C24 N5  C24 N5 53 1450 3.75 N5  54 1435 3.82 3.49 3.72 3.55 C19 N5  C19 N5  55 14413.85 3.55 3.75 3.6  C20 N5  C20 N5  56 1411 3.86 3.89 3.6 3.82 3.7  C20N3  N5  C20 N5  57 1149 3.89 3.54 3.72 3.89 3.66 3.67 3.63 3.47 C2  C3 C8  N1  C2  C3  C8  N1  TABLE A2-14: van der Waals Amino Acid GLY SERMASP-2 AA# 656 657 AA atom N O C 1 1129 3.87 3.77 3.3  3.39 3.79 3.8 3.75 C16 C15 C23 C09 C05 C23 N20 2 1034 3.69 3.27 3.51 3.51 C24 C09 C05N19 3 1024 3.66 3.59 3.84 3.49 3.72 3.77 C18 C17 C16 C3  C2  N5  4 10593.68 3.5  3.41 3.75 3.83 3.78 3.74 C21 C20 C9  C4  C3  N5  N3  5 10883.77 3.6  3.73 3.35 3.86 3.64 C27 C25 C24 C08 C06 N18 6 1036 3.75 3.413.26 3.53 3.86 3.29 3.55 3.57 C23 C22 C21 C20 C19 C04 C02 N26 7 10813.71 3.79 3.41 3.58 3.81 3.62 C25 C23 C22 C21 C02 N26 8 1063 3.81 3.883.45 3.4  3.79 3.46 3.46 3.69 3.07 3.75 C23 C22 C21 C20 C19 C5  C4  C2 C1  N5  9 1065 3.82 3.61 3.55 3.06 3.68 3.64 C27 C25 C24 C05 C04 C01 101030 3.77 3.78 3.65 3.84 3.82 C19 C18 C3  C2  N4  11 1037 3.86 3.86 3.663.57 3.86 3.73 C14 C13 C22 C02 C01 N18 12 1118 3.67 3.58 3.62 3.79 3.8 C18 C17 C4  C2  N4  13 1007 3.71 3.85 3.87 C3  C11 N5  14 Melagatran3.9  3.72 3.25 3.81 3.68 3.77 999 C21 C20 C28 C6  C28 N25 15 1090 3.833.74 3.8  3.41 3.38 3.88 3.83 3.16 3.87 3.7  C22 C15 C12 C13 C14 C1  C3 C4  C13 N5  16 1089 3.47 3.48 3.85 2.95 3.86 C17 C18 C19 C2  N5  17 10213.58 3.47 3.75 3.85 3.79 3.55 C1  C2  C3  C11 C12 N3  18 1097 3.76 3.8 3.84 3.71 3.64 3.84 3.52 C18 C19 C1  C2   C3  C6  N6  19 54 3.78 3.643.68 C02 C08 N15 20 1042 3.67 3.76 3.47 3.39 3.85 3.7  3.53 3.49 C16 C17C01 C02 C17 C18 N03 N21 21 2018 3.74 3.78 3.3  3.7  C21 C22 C9  N4  221031 3.76 3.82 3.83 3.76 3.3  3.7  C20 C21 C24 C25 C10 N11 23 1153 3.753.82 3.79 3.56 3.66 C1  C2  C12 C13 C14 24 1025 3.46 3.54 2.68 C14 C17C18 25 1012 3.64 3.85 3.11 3.54 3.81 C17 C1  C2  C3  N5  26 1078 3.873.63 3.59 3.79 2.71 C18 C19 C20 C21 C5  27 1145 3.61 3.62 3.47 3.8  3.593.83 3.75 C27 C28 C13 C3  C4  C13 N5  28 1050 3.74 3.68 3.89 3.89 3.653.53 3.79 3.76 C6  C7  C8  C12 C13 C15 N4  N5  29 1253 3.55 3.79 3.793.15 3.82 C02 C16 C20 C21 N07 30 1257 3.53 3.88 3.9  3.8  3.04 3.85 C02C03 C06 C03 C19 N08 31 1297 3.65 3.78 3.79 3.66 3.29 C23 C24 C1  C4  C5 32 1304 3.9  3.53 3.64 3.14 C18 C19 C5  C6  33 1306 3.86 3.83 3.78 3.623.14 3.86 C19 C2  C3  C5  C6  N5  34 1307 3.8  3.54 3.54 3.85 3.87 3.493.11 C18 C19 C20 C21 C3  C5  C6  35 1328 3.78 3.48 3.76 3.8  3.8  3.4 3.16 3.5  C18 C19 C20 C20 C3  C5  C6  N5  36 1334 3.7  3.72 3.58 3.21C19 C20 C5  C6  37 1335 3.74 3.7  3.75 3.72 3.83 3.74 C1  C2  C11 C13N3  N6  38 1338 3.57 3.85 3.64 3.21 3.89 C23 C3  C5  C6  N5  39 13453.89 3.7  3.76 3.62 3.78 C26 C27 C28 C16 C5  40 1351 3.49 3.84 3.61 3.183.83 C25 C3  C5  C6  N5  41 1353 3.55 3.87 3.81 3.44 3.33 3.87 C19 C20C1  C4  C5  N5  42 1367 3.54 3.87 3.78 3.71 3.82 C8  C9  C1  C9  N4  431368 3.66 3.55 3.18 3.82 3.89 3.88 C35 C07 C09 C21 C36 N38 44 1371 3.643.79 3.89 3.78 3.77 3.38 3.85 3.87 C19 C20 C2  C3  C5  C6  N2  C23 451372 3.52 3.78 3.14 3.84 C9  C13 C14 N4  46 1373 3.86 3.51 3.88 3.883.75 3.2  3.84 C18 C19 C20 C3  C5  C6  N5  47 1492 3.56 3.73 3.69 3.793.37 3.38 3.79 C21 C22 C3  C4  C5  C6  N5  48 1399 3.83 3.5  3.88 3.823.16 3.82 C21 C22 C23 C3  C4  N5  49 1406 3.56 3.65 3.13 3.84 C20 C6 C7  N5  50 1433 3.69 3.61 3.83 3.75 3.32 C1  C5  C12 C15 C16 51 14 3.593.47 C10 C9  52 1360 3.66 3.6  3.13 C24 C5  C6  53 1450 3.61 3.62 3.893.65 3.65 3.78 3.28 C19 C20 C1  C2  C3  C4  C5  54 1435 3.58 3.88 3.553.1  3.85 C19 C3  C5  C6  N5  55 1441 3.61 3.24 3.08 3.89 3.79 3.88 3.88C20 C10 C11 C6  C9  C11 N5  56 1411 3.66 2.92 3.76 3.88 3.37 3.88 3.67C20 C23 C5  C8  C9  C23 N5  57 1149 3.72 3.5  3.8  3.78 3.66 3.68 C2 C3  C4  C14 C3  N2  Amino Acid SER MASP-2 AA# 657 AA atom CA CB N O OG 11129 3.84 3.56 3.63 C24 C23 C16 2 1034 3.68 3.9  3.56 N19 C18 C14 3 10243.86 3.44 C20 C16 4 1059 3.59 3.67 3.79 C22 C22 C20 5 1088 3.6  3.1 3.19 C28 C28 C27 6 1036 3.73 3.83 3.77 3.41 N26 C25 C25 C23 7 1081 3.863.85 N26 C23 8 1063 3.8  3.5  C23 C39 9 1065 3.59 C17 10 1030 11 10373.84 3.47 C17 C15 12 1118 3.77 C19 13 1007 3.51 C3  14 Melagatran 3.8 3.55 999 C23 C19 15 1090 3.57 3.77 3.41 3.46 3.78 N5  N4  C23 C13 C22 161089 3.58 C17 17 1021 18 1097 3.68 3.66 3.85 3.28 N6  C22 C19 C20 19 543.6  3.57 C14 C14 20 1042 3.75 3.73 3.79 3.3  3.69 N03 N21 C20 C18 C2021 2018 3.89 3.36 3.79 N4  C23 C25 22 1031 23 1153 3.39 C1  24 1025 3.58C07 25 1012 3.55 3.41 C17 C18 26 1078 27 1145 3.74 C26 28 1050 3.62 C8 29 1253 3.5  3.29 C02 C03 30 1257 3.52 3.39 C02 C03 31 1297 3.64 3.37C23 C24 32 1304 3.52 3.31 C19 C20 33 1306 3.61 3.64 C21 C23 34 1307 3.733.55 C23 C23 35 1328 3.28 3.34 C19 C20 36 1334 37 1335 3.89 3.85 3.54N6  C23 C6  38 1338 3.48 3.26 C23 C24 39 1345 3.85 3.75 3.86 C29 C7  C9 40 1351 3.47 3.31 C25 C26 41 1353 3.52 3.28 C19 C20 42 1367 3.52 3.32C8  C9  43 1368 3.54 3.32 C35 C36 44 1371 45 1372 3.3  3.5  C8  C9  461373 3.5  3.31 C19 C20 47 1492 3.82 3.69 3.53 3.84 3.51 3.75 N7  N7  C23C21 C23 C23 48 1399 3.46 3.24 C22 C23 49 1406 3.4  3.21 C20 C23 50 143351 14 3.82 3.82 C10 C9  52 1360 3.53 3.32 C24 C25 53 1450 3.89 3.58 C24C24 54 1435 3.46 3.29 C19 C20 55 1441 3.49 3.28 C20 C21 56 1411 3.233.28 C19 C20 57 1149 3.51 3.75 3.15 3.44 C8  C2  C3  C8  TABLE A2-15:van der Waals Amino Acid MET MASP-2 AA# 658 AA atom C CA CB CE CG 1 11293.89 O25 C24 O26 2 1034 3.72 3.76 3 1024 4 1059 5 1088 6 1036 7 1081 81063 9 1065 10 1030 11 1037 12 1118 13 1007 14 Melagatran 3.83 3.84 999C28 O30 15 1090 16 1089 17 1021 3.74 N3  18 1097 19  54 20 1042 21 201822 1031 23 1153 3.86 3.79 C28 C28 24 1025 25 1012 26 1078 27 1145 3.813.81 3.87 3.58 3.28 3.84 3.46 3.2  3.28 3.59 3.8  3.74 3.3  3.23 3.33C17 C13 C15 C16 C17 C18 C16 C17 C18 C19 C20 C21 C19 C20 O1 28 1050 291253 30 1257 31 1297 32 1304 33 1306 34 1307 3.64 C6  35 1328 36 1334 371335 38 1338 39 1345 3.77 3.79 3.83 3.75 C9  C6  C8  C9  40 1351 41 135342 1367 43 1368 44 1371 45 1372 46 1373 47 1492 48 1399 49 1406 50 143351 14 3.37 C2  52 1360 53 1450 54 1435 55 1441 3.71 C11 56 1411 3.8 3.79 3.47 C23 C25 O3  57 1149 3.69 3.58 C15 C16 Amino Acid MET MASP-2AA# 658 AA atom CG N O  1 1129  2 1034  3 1024  4 1059  5 1088  6 1036 7 1081  8 1063  9 1065 3.85 C05 10 1030 11 1037 12 1118 13 1007 14Melagatran 3.52 999 C28 15 1090 16 1089 17 1021 18 1097 3.69 C3  19  5420 1042 21 2018 22 1031 23 1153 24 1025 3.41 C18 25 1012 3.86 C2  261078 3.72 C5  27 1145 3.68 3.44 3.56 C13 C17 C18 28 1050 29 1253 30 125731 1297 32 1304 33 1306 34 1307 35 1328 3.76 C6  36 1334 37 1335 38 13383.89 C6  39 1345 3.32 3.48 C10 C9  40 1351 41 1353 3.74 C5  42 1367 431368 3.65 C09 44 1371 3.83 C6  45 1372 46 1373 47 1492 48 1399 49 140650 1433 51 14 52 1360 53 1450 54 1435 3.89 C6  55 1441 3.61 C11 56 14113.56 C23 57 1149 3.74 C21 TABLE A2-16: van der Waals Amino Acid Met ASNCYS MASP-2 AA# 658 659 660 AA atom SD C CA CB SG  1 1129 3.55 3.54 3.713.43 3.45 3.35 3.63 N19 N19 C18 N20 C18 C16 C15  2 1034  3 1024  4 10593.72 N6   5 1088 3.86 3.84 3.78 C28 N29 C28  6 1036 3.7  3.63 N26 N26  71081  8 1063  9 1065 3.64 3.78 C05 N28 10 1030 3.74 3.76 3.5  N4  N4 C17 11 1037 3.6  3.51 N18 12 1118 N1  3.84 N4  13 1007 14 Melagatran 99915 1090 16 1089 3.49 3.66 N5  N5  17 1021 18 1097 3.85 N6  19  54 3.753.53 3.22 3.67 N15 C14 N13 N15 20 1042 21 2018 3.84 N4  22 1031 23 11533.8  3.62 C8  N1  24 1025 3.78 N09 25 1012 3.7  3.68 3.53 C17 C18 N5  261078 27 1145 3.83 3.83 C30 N4  28 1050 3.78 C8  29 1253 3.55 3.6  3.33C02 C03 N07 30 1257 3.83 N08 31 1297 32 1304 3.86 N5  33 1306 3.65 3.213.63 3.61 3.02 3.42 C23 N4  N5  C23 N4  N4  34 1307 3.66 C23 35 13283.42 3.61 2.92 N5  C19 N5  36 1334 3.75 N4 37 1335 3.64 C6  38 1338 3.83N5  39 1345 3.69 3.8  3.34 3.87 3.6  3.7  N6  C10 C29 C31 C9  N6  401351 3.68 3.66 3.55 C25 C26 N5  41 1353 42 1367 43 1368 3.74 3.36 N38N38 44 1371 3.55 3.78 3.8 N5  N4  N6  45 1372 3.82 3.54 N4  N4  46 13733.82 N5  47 1492 3.9  3.72 C23 N7  48 1399 49 1406 3.78 N5  50 1433 5114 3.82 C2  52 1360 53 1450 3.77 3.39 C24 C24 54 1435 3.88 3.88 N5  N5 55 1441 3.78 N5  56 1411 3.73 3.56 N5  N5  57 1149 3.39 3.76 N2  N2 Amino Acid GLN GLY TYR MASP-2 AA# 665 667 669 AA atom CD OE1 C CA N CZCE1 CE2  1 1129 3.68 3.36 C18 N19  2 1034 3.78 3.47 3.32 N19 C18 N20  31024 3.47 N4   4 1059 3.68 N4   5 1088 3.35 N31  6 1036 3.44 N27  7 10813.86 N27  8 1063 3.76 N4   9 1065 3.48 N29 10 1030 3.44 N5  11 1037 3.46N19 12 1118 3.53 N5  13 1007 14 Melagatran 3.49 999 N24 15 1090 16 10893.35 3.73 C22 N4  17 1021 3.7  3.82 3.89 Cl1 Cl1 Cl1 18 1097 3.5  N5  19 54 3.84 3.42 3.87 C12 N11 C12 20 1042 3.87 N22 21 2018 3.66 3.47 3.4 N4  C25 N5  22 1031 23 1153 3.31 N2  24 1025 25 1012 26 1078 3.67 3.463.47 3.49 Cl1 Cl1 Cl1 Cl1 27 1145 3.33 N4  28 1050 3.27 N3  29 1253 301257 31 1297 32 1304 33 1306 34 1307 3.89 3.63 3.44 3.67 3.8  Cl1 Cl1Cl1 Cl1 Cl1 35 1328 36 1334 3.65 3.65 3.69 C23 Cl1 Cl1 37 1335 3.9  3.723.45 N6  C23 N5  38 1338 39 1345 3.85 3.56 3.68 N6  C31 N5  40 1351 411353 42 1367 43 1368 44 1371 3.67 3.34 3.64 3.71 Cl1 Cl1 Cl1 Cl1 45 137246 1373 47 1492 3.65 N6  48 1399 49 1406 50 1433 3.7  3.69 3.58 3.83 C6 Cl1 Cl1 Cl1 51 14 52 1360 53 1450 3.6  3.72 3.56 3.77 3.9  C22 Cl1 Cl1Cl1 Cl1 54 1435 55 1441 56 1411 57 1149 3.19 N1 

TABLE A3 Resolution Space Unit Cell # Compound Construct [Å] Groupparameters 1 Melagatran CCP2-SP 2.31 C121 a = 72.6, b = 40.8, c = 103.4,beta = 98.45 999 2 1129 CCP2-SP 1.90 C2221 a = 41.1, b = 72.5, c = 267.13 1088 CCP2-SP-HIS 1.17 P1211 a = 40.82, b = 76.72, c = 50.53, b =105.09 4 1036 CCP2-SP-HIS 1.69 P1211 a = 40.59, b = 75.96, c = 50.87, a= 90, b = 105.21, c = 90.0 5 1024 CCP2-SP 2 C121 a = 72.34, b = 41.26, c= 110.59, a = 90.0, b = 106.2, g = 90.0 6 1037 CCP2-SP 1.88 P65 a =41.61, b = 41.61, c = 326.15, a = 90, b = 90, g = 120 7 1081 CCP2-SP 2.5P1 a = 39.62, b = 41.69, c = 51.34, a = 78.25, b = 86.48, g = 64.20 81065 CCP2-SP-HIS 1.70 P212121 a = 40.64, b = 50.83, c = 137.20, a = 90,b = 90, g = 90 9 1034 CCP2-SP-HIS 2.7 P6122 a = 83.29, b = 83.29, c =150.80, a = 90, b = 90, g = 120 10 1059 CCP2-SP-HIS 1.90 I222 a = 73.62,b = 99.42, c = 105.36, a = 90, b = 90, g = 90 11 1030 CCP2-SP-HIS 1.8I222 a = 74.04, b = 99.58, c = 106.24, a = 90, b = 90, g = 90 12 1118CCP2-SP-HIS 1.20 P1 a = 39.64, b = 42.06, c = 51.38, a = 78.45, b =86.21, g = 63.56 13 1063 CCP2-SP-HIS 2.5 P1 a = 39.34, b = 41.65, c =51.18, a = 77.87, b = 85.71, g = 63.57 14 1007 CCP2-SP-HIS 2.50 P1 a =41.13, b = 41.23, c = 119.53, a = 87.46, b = 82.51, g = 61.13 15 1090CCP2-SP-HIS 2.3 P21 a = 40.50, b = 76.50, c = 50.64, a = 90, b = 105.24,g = 90 16 1089 CCP2-SP-HIS 1.10 P21 a = 40.64, b = 76.04, c = 50.67, a =90, b = 105.31, g = 90 17 1021 CCP2-SP-HIS 2.3 C2221 a = 72.14, b =40.68, c = 102.91, a = 90, b = 98.14, g = 90 18 1097 CCP2-SP-HIS 1.90P21 a = 55.54, b = 75.63, c = 71.86, a = 90, b = 102.69, g = 90 19 1297CCP2-SP-HIS 2 P1 a = 50.63, b = 99.39, c = 138.7, a = 90.17, b = 90.24,g = 90.16 20 1304 CCP2-SP-HIS 1.30 P212121 a = 51.70, b = 71.61, c =79.83, a = 90, b = 90, g = 90 21 1306 CCP2-SP-HIS 2 P61 a = 84.11, b =84.11, c = 156.08, a = 90.00, b = 90.00, g = 90.00 22 1307 CCP2-SP-HIS1.54 P212121 a = 51.24, b = 71.10, c = 79.16, a = 90, b = 90, g = 90 231328 CCP2-SP-HIS 2.71 P1211 a = 75.44, b = 128.52, c = 84.66, a = 90, b= 108.58, g = 90 24 1334 CCP2-SP-HIS 1.67 P1 a = 39.52, b = 41.90, c =51.02, a = 78.01, b = 85.84, g = 63.92 25 1335 CCP2-SP-HIS 1.5 P212121 a= 38.06, b = 68.48, c = 117.67, a = 90, b = 90, g = 90 26 1338CCP2-SP-HIS 1.49 P1 a = 40.54, b = 41.78, c = 53.96, a = 86.44, b =81.35, g = 61.04 27 1345 CCP2-SP-HIS 2 P61 a = 84.12, b = 84.12, c =156.10, a = 90.00, b = 90, g = 120 28 1351 CCP2-SP-HIS 2.00 P212121 a =60.80, b = 62.80, c = 93.87, a = 90.00, b = 90.00, g = 90.00 29 1353CCP2-SP-HIS 1.2 P212121 a = 51.36, b = 71.52, c = 81.32, a = 90, b = 90,g = 90 30 1367 CCP2-SP-HIS 1.54 P212121 a = 51.60, b = 71.42, c = 79.38,a = 90, b = 90, g = 90 31 1368 CCP2-SP-HIS 1.38 P212121 a = 51.63, b =71.60, c = 79.19, a = 90, b = 90, g = 90 32 1371 CCP2-SP-HIS 2.30 C121 a= 73.03, b = 41.12, c = 108.70, a = 90, b = 106.51, g = 90 33 1372CCP2-SP-HIS 1.3 P212121 a = 51.71, b = 71.71, c = 79.67, a = 90, b = 90,g = 90 34 1373 CCP2-SP-HIS 1.40 P212121 a = 51.65, b = 71.58, c = 79.78,a = 90, b = 90, g = 90 35 1492 CCP2-SP-HIS 2.2 P61 a = 83.60, b = 83.60,c = 154.39, a = 90, b = 90, g = 120 36 1399 CCP2-SP-HIS 1.50 P212121 a =51.64, b = 71.47, c = 79.62, a = 90, b = 90, g = 90 37 1406 CCP2-SP-HIS1.84 P212121 a = 51.55, b = 71.49, c = 79.77, a = 90, b = 90, g = 90 38 54 CCP2-SP-HIS 1.85 P212121 a = 37.76, b = 68.38, c = 118.06, a = 90, b= 90, g = 90 39 2018 CCP2-SP 1.48 P212121 a = 51.43, b = 71.49, c =79.01, a = 90, b = 90, g = 90 40 1031 CCP2-SP-HIS 3.00 P4212 a = 142.10,b = 142.10, c = 174.33, a = 90, b = 90, g = 90 41 1153 CCP2-SP-HIS 2.3P6122 a = 83.05, b = 83.05, c = 149.46, a = 90, b = 90, g = 120 42 1025CCP2-SP-HIS 2.45 P1 a = 50.279, b = 99.140, c = 138.454, a = 90.01, b =90.01, g = 90.00 43 1012 CCP2-SP-HIS 1.8 P212121 a = 50.71, b = 102.21,c = 137.53, a = 90, b = 90, g = 90 44 1078 CCP2-SP-HIS 2.90 P1211 a =92.20, b = 180.97, c = 196.95, a = 90, b = 92.5, g = 90 45 1145CCP2-SP-HIS 1.9 P212121 a = 38.23, b = 68.15, c = 117.16, a = 90, b =90, g = 90 46 1050 CCP2-SP-HIS 2.50 P212121 a = 37.80, b = 67.96, c =116.92, a = 90, b = 90, g = 90 47 1253 CCP2-SP 1.3 P212121 a = 51.30, b= 71.56, c = 79.40, a = 90, b = 90, g = 90 48 1257 CCP2-SP 1.10 P1211 a= 40.86, b = 75.91, c = 51.05, a = 90, b = 105.47, g = 90 49  14CCP2-SP-HIS 1.8 P212121 a = 37.94, b = 69.14, c = 117.53, a = 90, b =90, g = 90 50 1042 CCP2-SP-HIS 2.25 P31 a = 83.758, b = 83.758, c =153.239, a = 90.00, b = 90.00, g = 120.00 51 1433 CCP2-SP-HIS 1.4P212121 a = 51.62, b = 71.81, c = 79.86, a = 90, b = 90, g = 90 52 1360CCP2-SP-HIS 1.40 P212121 a = 51.71, b = 71.95, c = 82.20, a = 90, b =90, g = 90 53 1450 CCP2-SP-HIS 1.4 P212121 a = 51.73, b = 71.79, c =79.73, a = 90, b = 90, g = 90 54 1435 CCP2-SP-HIS 1.50 P212121 a =51.66, b = 71.54, c = 79.96, a = 90, b = 90, g = 90 55 1441 CCP2-SP-HIS1.40 P212121 a = 51.48, b = 71.24, c = 79.57, a = 90, b = 90, g = 90 561411 CCP2-SP-HIS 1.60 P212121 a = 51.51, b = 71.35, c = 79.80, a = 90, b= 90, g = 90 57 1149 CCP2-SP-HIS 2.8 P 61 2 2 a = 80.11, b = 80.11, c =150.17, a = 90, b = 90, c = 120

TABLE A4 Table A4-1: Ligand-pharmacophore element distancesPharmacophore element compounds C2 C3 C4 C5 C6 C7 CA1 CA2 CA3 CA4 CA5CA6 1 14 0 0 0 0 0 0 1.47 0 0 0 0 1.68 2 999_1 2.69 0 0 0 0 0 0.48 0 0 00 0 3 999_2_A 2.87 0 0 0 0 0 0.6 0 0 0 0 0 4 999_2_B 2.86 0 0 0 0 0 0.570 0 0 0 0 5 54_A 0 4.06 0 0 0 0 0.6 0 0 0 0 0 6 54_B 4 0 0 0 0 0 0.49 00 0 0 0 7 1129 3.15 0 0 0 0 0 0.35 0 0 0 0.67 0 8 1034 2.4 0 0 0 0 00.28 0 0 0 0.98 0 9 1024 0 0 0 0 0 0 0.4 0.33 0 0 0 0 10 1042_1 1.81 0 00 0 0 0.87 0.48 0 0 0 0 11 1042_2 1.33 0 0 0 0 0 0.5 0.72 0 0 0 0 121042_3 2.05 0 0 0 0 0 0.5 1.65 0 0 0 0 13 2018 0 9.61 0 0 0 0 0.54 0 0 01.25 1.35 14 1059 1.86 0 0 0 0 0 1.27 0.8 0 0 0 0 15 1088_A 1.75 0 0 0 00 0.4 0 0 0 0.39 0 16 1088_B 1.93 0 0 0 0 0 0.62 0.2 0 0 0 0 17 1036_1 00 0 0 0 0 0.35 0 0 0 1 0 18 1036_2_1 0 0 0 0 0 0 0.47 0 0 0 0.78 0 191036_2_2 0 0 0 0 0 0 0.54 0 0 0 1.25 0 20 1081 0 0 1.99 0 0 0 0.48 0.760 0 0 0 21 1063 0.48 0 0 0 0 0 0.3 0.85 0 0 0 0 22 1065 0.11 0 0 0 0 00.88 0.1 0 0 0 0 23 1030_A 0 0 0 0 0 0 0.34 0 0 0 4.24 3.19 24 1030_B 00 0 0 0 0 0.39 0 0 0 1.57 0 25 1037 0 0 0 0 0 0 0.27 0 0 0 1.21 0 261118 0 0 2.54 0 1.17 0 0.43 0.69 0 0 0 0 27 1090 0 0 0 0 0 0 0.98 0 0 00.91 0 28 1007_1 0 0 0 0 0 0 0.35 0.77 0 0 0 0 29 1007_2 0 0 0 0 0 00.59 0.86 0 0 0 0 30 1149 0 0 3.8 0 0 0 0.35 0 0 1.47 0 4.96 31 1021_A 00 0 0.53 0 0 1.4 0 0 0 3.03 0 32 1021_B 0 0 0 0.45 0 0 1.36 0.48 0 0 0 033 1097_1 0.69 0 0 0 0 0 0.29 0 0 0 0.98 0 34 1097_2 0.72 0 0 0 0 0 0.320 0 0 1.1 0 35 1031_1 0 0 0 0.34 0 0 1.42 0.36 0 0 0 0 36 1031_2 0 0 00.41 0 0 1.56 0.6 0 0 0 0 37 1031_3 0 0 0 0.48 0 0 1.56 0.44 0 0 0 0 381031_4 0 0 0 0.3 0 0 1.41 0.5 0 0 0 0 39 1153_A 8.69 0 0 0 0 0 0.43 0.344.19 0 0 0 40 1153_B 10.14 0 0 0 0 0 0.39 0.58 0 0 6.17 0 41 1025_1 0.840 0 0 0 0 0.49 0.53 0 0 0 0 42 1025_2 0.79 0 0 0 0 0 0.98 0.18 0 0 0 043 1025_3 0.49 0 0 0 0 0 0.81 0.86 0 0 0 0 44 1025_4 0.51 0 0 0 0 0 0.280.97 0 0 0 0 45 1025_5 0.67 0 0 0 0 0 0.62 0.37 0 0 0 0 46 1025_6 0.52 00 0 0 0 1.03 0.55 0 0 0 0 47 1089_A 0 0 0 0 0 0 1 0.89 0 0 0 0 48 1089_B0 0 0 0 0 0 0.99 0 0 0 1.16 0 49 1012_1 0 0 0 0 0 0 0.4 0 0 0 1.27 0 501012_2 0 0 0 0 0 0 0.44 0 0 0 0.94 0 51 1078_1 0.69 0 0 0.4 0 0 1.580.48 0 0 0 0 52 1078_10 0.49 0 0 0.3 0 0 1.34 0.49 0 0 0 0 53 1078_110.6 0 0 0.41 0 0 1.64 0.64 0 0 0 0 54 1078_12 0.4 0 0 0.52 0 0 1.43 0.640 0 0 0 55 1078_13 0.58 0 0 0.47 0 0 1.62 0.73 0 0 0 0 56 1078_14 0.74 00 0.47 0 0 1.61 0.8 0 0 0 0 57 1078_15 0.81 0 0 0.43 0 0 1.56 0.65 0 0 00 58 1078_16 0.64 0 0 0.42 0 0 1.49 0.49 0 0 0 0 59 1078_2 0.61 0 0 0.460 0 1.55 0.61 0 0 0 0 60 1078_3 0.43 0 0 0.45 0 0 1.53 0.27 0 0 0 0 611078_4 0.67 0 0 0.52 0 0 1.62 0.59 0 0 0 0 62 1078_5 0.71 0 0 0.42 0 01.76 0.6 0 0 0 0 63 1078_6 1.09 0 0 0.48 0 0 1.31 0.65 0 0 0 0 64 1078_70.64 0 0 0.61 0 0 1.69 0.55 0 0 0 0 65 1078_8 0.85 0 0 0.78 0 0 1.670.92 0 0 0 0 66 1078_9 0.67 0 0 0.46 0 0 1.62 0.56 0 0 0 0 67 1145_A 0 00 0 0 0 0.47 0.41 1.22 0 0 0 68 1145_B 0 0 0 0 0 0 0.47 0.41 1.22 0 0 069 1050 6.95 0 0 0 0 0 0.57 0.33 0 0 0 0 70 1253 0.28 0.07 0 0 0 0 0.590.23 0 0 0 0 71 1257 0 0.1 0 0 0.53 0 0.65 0 0 0 1.2 0 72 1297_1 0.340.3 0 0 0 0 0.39 0.19 0 1.24 0 0 73 1297_2 0.34 0.17 0 0 0 0 0.47 0.22 01.25 0 0 74 1297_3 0.28 0.23 0 0 0 0 0.33 0.22 0 0.94 0 0 75 1297_4 0.310.18 0 0 0 0 0.48 0.24 0 0.98 0 0 76 1297_5 0.24 0.29 0 0 0 0 0.44 0.070 1.22 0 0 77 1297_6 0.33 0.4 0 0 0 0 0.36 0.24 0 1.14 0 0 78 1304 00.09 0 0 0 0 0.56 0.23 0 0 0 0 79 1306_1 0 0 0 0 0 0 0.05 0.6 0 0 0 0 801306_2 0 0 0 0 0 0 0.74 1.14 0 0 0 0 81 1307 0 0 0 0.37 0 0.76 1.55 0.170 0 0 0 82 1328_1 0 0.4 0.76 0 0 0 0.49 0.5 0 0 0 0 83 1328_2 0 0.151.28 0 0 0 0.41 0.43 0 0 0 0 84 1328_3 0 0.21 1.76 0 0 0 0.4 0.48 0 0 00 85 1328_4 0 0.18 1.86 0 0 0 0.5 0.3 0 0 0 0 86 1334 0 0 0 0.34 0 01.04 0.7 0 0 0 0 87 1335 0 0 0 0 0 0 0.38 0.56 0 0 0 0 88 1338 0 0.12 00 0 0 0.55 0.59 0 1.21 0 0 89 1345_1 0 0 0 0 0 0 0.51 1.2 1.44 0 0 0 901345_2 0 0 0 0 0 0 0.45 0.89 1.13 0 0 0 91 1351 0 0.12 0 0 0 0 0.57 0.80 3.3 0 0 92 1353 0.58 0.13 0 0 0 0 0.61 0.5 0 0 0 0 93 1360 0 0.11 0 00 0 0.57 2.35 0 0 1.11 0 94 1367 0 0.13 0 0 0 0 0.5 0.57 0 0 3.27 0 951368 0 0.16 0 0 0 0 0.62 0.95 0 0 2.23 0 96 1371 0 0 0 0.48 0 0 0.580.46 0 0 0 0 97 1372_A 0 0.09 1.91 0 0 0 0.55 0.47 0 0 0 0 98 1372_B 00.1 0 0 1.46 0 0.57 1.41 0 0 0 0 99 1373 0 0.08 0 0 0 0 0.56 0.54 0 02.5 0 100 1492 2.91 0 0 0 0 0 1.7 0 0 0 0.84 0 101 1399 0 0.14 0 0 0 00.59 0.85 0 2.39 0 0 102 1406 0 0.12 0 0 0 0 0.56 0.42 0 1.59 0 0 1031411 0.42 0.32 0 0 0 0 0.71 0.52 0 0 0 0 104 1433 0.26 0 0 0.2 0 0 0.980.18 0 0 0 0 105 1435 0 0.15 1.37 0 0.38 0 0.6 0.8 0 0 0 0 106 1441 0.540.17 0 0 0 0 0.64 0.64 0 0 0 0 107 1450_A 0 0 0 0.34 0 0.72 1.03 0.4 0 00 0 108 1450_B 0 0 0 1.67 0 1.3 0.94 1.24 0 0 0 0 Table A4-2:Ligand-pharmacophore element distances Pharmacophore element compoundsH1 H2 H3 H4 N1 N2 O1 O2 O3 O4 1 14 0 4.66 0 1.82 0 0 3.89 0.46 0 0 2999_1 0 0 4.95 3.36 1.77 0.72 1.53 0.41 0 0 3 999_2_A 0 0 4.85 3.24 1.710.89 1.86 0.53 0 0 4 999_2_B 0 0 4.73 3.33 1.63 1.1 1.77 0.77 0 0 5 54_A0 0 5.03 0 0 0 0 0 0 3.96 6 54_B 0 0 4.44 0 0 0 0 0 0 3.94 7 1129 0 01.34 3.79 1.8 1.8 0.39 0.58 0 0 8 1034 0 0 1.08 3.56 1.87 0.86 0.39 0.490 0 9 1024 0 0 4.93 3.21 1.74 0.59 0.4 0.4 0 0 10 1042_1 0 0 5.4 3.081.3 0.56 2.71 0.67 0 0 11 1042_2 0 0 5.3 3.52 1.61 1.72 3.1 0.75 0 0 121042_3 0 0 6.42 4.11 1.45 1.33 0 1.19 0 0 13 2018 0 0 7.09 1.03 2.16 02.54 2.38 0 0 14 1059 0 0 4.5 3.89 1.27 0.41 0.82 0.49 0 0 15 1088_A 0 03.41 5 0.89 0.36 0.57 0.41 0 0 16 1088_B 0 0 3.63 5.04 1.15 0.49 0.720.37 0 0 17 1036_1 0 0 5.87 3.25 1.78 0.45 0.38 0.34 0 0 18 1036_2_1 0 04.76 3.7 2.16 0.81 0.74 0.45 0 0 19 1036_2_2 0 0 5.81 3.32 2.08 0.66 0.80.68 0 0 20 1081 0 0 5.53 3.48 1.57 0.21 0.28 0.45 0 0 21 1063 0 0 4.663.47 1.56 1.21 0.6 0.68 0 0 22 1065 0 0 4.27 4.71 0.96 0.26 0.31 0.26 00 23 1030_A 0 0 3.05 3.42 1.55 0 0.5 0.57 0 0 24 1030_B 0 0 3.03 3.191.49 0 0.96 0.61 0 0 25 1037 0 0 3.03 3.2 1.98 0 0.66 0.53 0 0 26 1118 00 5.69 3.5 1.59 0.32 0.25 0.55 0 0 27 1090 0 0 5.6 0.54 1.59 0.46 0.530.47 0 0 28 1007_1 0 0 4.59 2.28 1.39 0.59 0.76 0.57 0 0 29 1007_2 0 04.59 2.16 1.55 1.03 0.89 0.77 0 0 30 1149 0 0 2.9 3.72 1.89 3.4 0.776.17 0 0 31 1021_A 0 0 0.8 1.73 0 0.95 1 0.87 0 0 32 1021_B 0 0 0.840.53 0 0.62 1.02 0.5 0 0 33 1097_1 0 0 2.07 3.33 1.92 0.61 0.51 0.44 0 034 1097_2 0 0 2.16 3.54 1.79 0.4 0.51 0.32 0 0 35 1031_1 0 1.6 1.16 2.790 0.64 0.91 0.63 0 0.92 36 1031_2 0 1.47 0.45 2.01 0 0.8 1.17 2.33 01.05 37 1031_3 0 1.36 1.16 2.79 0 0.3 1.05 0.83 0 0.97 38 1031_4 0 1.461.26 2.97 0 0.74 1.04 0.82 0 0.95 39 1153_A 0 0 0.44 4.25 1.41 0.34 1.730.79 7.39 0 40 1153_B 0 0 1.01 4.21 1.5 1.88 2.22 6.33 12.11 0 41 1025_10 0 2.07 3.53 1.74 0.97 2.51 2.94 0 0 42 1025_2 0 0 1.75 2.28 1.85 1.082.55 2.63 0 0 43 1025_3 0 0 1.7 3.95 1.06 0.59 1.27 3 0 0 44 1025_4 0 01.05 3.36 1.39 0.23 2.33 0.72 0 0 45 1025_5 0 0 2.04 3.68 0.4 0.91 1.122.96 0 0 46 1025_6 0 0 1.77 3.75 1.11 0.59 1.36 2.83 0 0 47 1089_A 0 05.67 0.59 1.52 0.5 0.41 0.42 0 0 48 1089_B 0 0 5.68 0.57 1.56 0.38 0.40.43 0 0 49 1012_1 0 0 4.44 2.79 1.21 0.32 0.39 0.42 0 0 50 1012_2 0 04.08 1.93 2.54 0.66 0.67 0.65 0 0 51 1078_1 0 0.54 0.94 1.67 0 0.64 1.050.43 0 1.26 52 1078_10 0 0.46 1.24 0.6 0 0.35 1.12 0.63 0 1.08 531078_11 0 0.5 0.5 1.68 0 0.3 1.35 0.7 0 1.19 54 1078_12 0 0.71 1 1.45 00.59 1.02 1 0 1.32 55 1078_13 0 0.71 1.11 0.63 0 0.2 1.24 0.51 0 1.38 561078_14 0 0.41 0.69 1.45 0 0.5 1.29 0.8 0 1.28 57 1078_15 0 0.41 0.851.59 0 0.61 1.2 0.69 0 1.34 58 1078_16 0 0.69 0.73 1.7 0 0.5 1.02 0.54 01.38 59 1078_2 0 0.34 0.59 1.74 0 0.35 1.19 0.55 0 0.98 60 1078_3 0 0.361.07 0.56 0 0.31 1.27 0.59 0 1.01 61 1078_4 0 0.67 0.39 1.67 0 0.33 1.170.51 0 1.28 62 1078_5 0 0.97 0.81 1.7 0 0.53 1.35 0.58 0 1.67 63 1078_60 0.61 1.78 1.01 0 1.38 1.26 0 0 1 64 1078_7 0 0.39 0.93 1.7 0 0.6 1.040.57 0 1.19 65 1078_8 0 0.46 0.74 1.57 0 0.58 1.21 0.73 0 1.36 66 1078_90 0.89 0.85 1.8 0 0.58 1.16 0.48 0 1.63 67 1145_A 0.1 0 4.73 3.44 1.470.31 0.23 0.61 2.39 0 68 1145_B 0.1 0 4.73 3.44 1.47 0.31 0.23 0.61 2.390 69 1050 0 0 0.65 3.44 1.43 0.26 0.59 0.42 0 0 70 1253 0 0 0.98 2.741.13 0.22 0.54 0.29 0 0 71 1257 0 0 0.74 2.6 1.22 0.23 0.61 0.29 0 0 721297_1 0 0 4.44 2.65 1.26 0.28 0.62 0.38 0 0 73 1297_2 0 0 4.23 2.771.12 0.14 0.6 0.37 0 0 74 1297_3 0 0 4.4 2.74 1.14 0.39 0.57 0.3 0 0 751297_4 0 0 4.27 2.72 1.17 0.19 0.57 0.38 0 0 76 1297_5 0 0 4.24 2.611.32 0.32 0.56 0.24 0 0 77 1297_6 0 0 4.25 2.58 1.39 0.88 0.6 0.28 0 078 1304 0 0 4.52 2.76 1.15 0.15 0.48 0.26 0 0 79 1306_1 0 0 4.93 4.212.05 0.66 1.07 0.19 0 0 80 1306_2 0 0 4.37 5.03 1.16 0.57 0.69 0.58 0 081 1307 0 0 0.82 0.55 0 0.56 1.43 0.73 0 0.83 82 1328_1 0 0 4.33 2.791.13 0.47 0.31 0.56 0 0 83 1328_2 0 0 4.58 2.68 1.16 0.17 0.48 0.39 0 084 1328_3 0 0 4.6 2.34 1.24 0.5 0.68 0.55 0 0 85 1328_4 0 0 4.56 2.551.1 0.61 1.12 0.58 0 0 86 1334 0 0 3.01 0.91 0 0.21 0.16 0.43 0 1.1 871335 0 0 4.98 1.46 1.65 0.36 2.14 0.29 0 0 88 1338 0 0 4.52 2.7 1.170.16 0.38 0.31 0 0 89 1345_1 0 0 5.45 3.64 1.98 1.06 1.1 0.38 2.93 0 901345_2 0 0 4.78 3.63 1.74 0.43 0.35 0.38 1.87 0 91 1351 0 0 4.36 2.691.21 0.31 0.43 0.39 0 0 92 1353 0 0 4.4 2.73 1.16 0.26 0.56 0.31 0 0 931360 0 0 4.55 2.82 1.1 0.18 0.59 0.27 0 0 94 1367 0 0 2.46 2.75 1.12 00.67 2 0 0 95 1368 0 0 3.8 2.77 1.11 0.24 0.6 5.09 0 0 96 1371 0 0 1.210.82 0 0.35 0.72 0.46 0 1.38 97 1372_A 0 0 1.18 2.8 1.11 0.16 0.53 0.240 0 98 1372_B 0 0 1.2 2.8 1.12 0.41 0.54 0.26 0 0 99 1373 0 0 4.46 2.771.11 0.22 0.51 0.26 0 0 100 1492 0 0 6 1.08 1.71 0 1.53 1.38 0 0 1011399 0 0 4.29 2.79 1.08 0.52 0.59 0.3 0 0 102 1406 0 0 4.51 2.81 1.020.33 0.56 0.38 0 0 103 1411 0 0 4.01 2.9 1.03 0.54 0.46 0.47 0 0 1041433 0 0 3.08 0.52 0 0.16 0.36 0.25 0 1.03 105 1435 0 0 4.44 2.75 1.10.18 0.49 0.23 0 0 106 1441 0 0 4.36 2.76 1.1 0.63 0.57 0.33 0 0 1071450_A 0 0 0.97 0.46 0 0.17 0.58 0.38 0 1.16 108 1450_B 0 0 1.04 0.36 00.24 0.5 0.38 0 0.53

TABLE A5 Table A5-1: Pharmacophore: Distance between elementsPharmacophore Region S2 Region S1 Region Elements d(H4, d(H4, d(O1,d(CA6, d(CA6, d(CA1, d(CA1, d(CA1, d(C3, d(CA1, d(CA1, d(CA1, d(O4, O1)O2) O2) O1) O2) O1) O2) N1) CA1) N1)2 O4) C5) H2) 1 14 3.02 3.13 5.287.02 3.51 3.49 3.51 2 999_1 3.57 4.90 2.29 3.61 4.51 3.61 3 999_2_A 3.495.01 2.30 3.58 4.73 3.64 4 999_2_B 3.18 5.07 2.52 3.35 4.89 3.60 5 11295.00 4.63 3.49 4.47 4.37 3.60 6 1034 4.86 4.31 3.48 4.35 4.19 3.64 71024 3.99 3.27 3.23 4.37 4.23 3.55 8 1042_1 3.35 3.67 3.40 3.98 4.133.58 9 1042_2 4.02 4.01 3.46 4.47 4.74 3.61 10 1042_3 4.90 4.54 3.63 112018 3.89 5.39 4.92 2.73 2.50 7.59 6.76 3.56 12 1059 4.89 4.48 3.20 5.325.00 1.85 13 1088_A 6.97 5.89 3.49 5.33 4.61 14 1088_B 6.73 6.06 3.025.22 4.78 15 1036_1 4.04 3.64 3.31 4.41 4.55 3.60 16 1036_2_1 4.42 3.443.17 4.62 4.33 3.66 17 1036_2_2 4.14 3.26 3.29 4.55 4.34 3.61 18 10815.10 4.46 3.45 4.57 4.27 3.62 19 1063 5.37 3.82 3.31 4.95 3.58 3.56 201065 6.39 5.35 3.30 4.32 4.20 3.47 21 1030_A 5.04 4.57 3.20 5.19 3.404.56 4.46 22 1030_B 4.76 4.55 3.30 4.31 4.50 23 1037 4.16 3.07 3.31 4.494.30 3.64 24 1118 4.85 4.52 3.25 4.35 4.33 3.55 25 1090 3.15 3.68 3.385.59 5.11 26 1007_1 3.59 2.73 3.55 4.39 3.86 1.38 27 1007_2 3.69 2.763.63 4.52 4.00 1.38 28 1149 5.59 8.32 8.70 7.04 8.45 5.15 9.42 3.57 291021_A 2.33 2.48 3.05 4.71 4.16 3.10 30 1021_B 3.14 3.94 3.20 4.52 4.583.11 31 1097_1 3.88 3.35 3.32 4.28 4.28 3.53 32 1097_2 4.74 4.28 3.334.35 4.09 3.52 33 1031_1 2.48 3.90 3.55 5.66 4.45 2.84 3.16 0.96 341031_2 2.45 3.99 3.45 5.53 7.12 2.73 3.08 0.96 35 1031_3 2.45 3.87 3.435.37 4.35 2.79 3.16 0.96 36 1031_4 2.53 3.54 3.29 5.59 4.22 2.71 3.090.96 37 1153_A 6.25 4.36 4.62 5.79 4.38 3.54 38 1153_B 5.77 7.90 9.575.51 8.18 3.54 39 1025_1 5.36 5.79 5.16 5.54 5.58 1.36 40 1025_2 4.524.59 4.97 5.40 4.61 1.35 41 1025_3 4.84 4.68 4.91 5.60 4.57 1.36 421025_4 4.83 3.57 2.98 5.48 3.79 1.36 43 1025_5 4.66 5.13 4.84 5.62 5.311.37 44 1025_6 4.98 4.26 5.71 6.05 4.12 1.36 45 1089_A 3.13 3.70 3.345.75 5.19 46 1089_B 3.14 3.69 3.33 5.68 5.17 47 1012_1 4.36 3.79 3.514.38 3.84 1.39 48 1012_2 2.36 2.42 3.35 4.38 3.81 1.39 49 1078_1 2.292.61 3.05 4.56 4.72 2.75 3.12 0.97 50 1078_10 3.11 3.46 2.72 4.35 4.372.76 3.12 0.97 51 1078_11 2.26 2.51 3.42 4.69 4.58 2.75 3.12 0.97 521078_12 3.08 3.40 2.81 4.34 4.51 2.74 3.12 0.98 53 1078_13 3.14 3.663.25 4.37 4.66 2.76 3.12 0.98 54 1078_14 2.48 2.59 2.91 4.46 4.47 2.753.13 0.97 55 1078_15 2.66 2.49 2.93 4.59 4.59 2.74 3.13 0.97 56 1078_162.20 2.69 3.11 4.42 4.54 2.74 3.13 0.97 57 1078_2 2.19 2.44 3.25 4.694.62 2.75 3.12 0.97 58 1078_3 3.13 3.61 3.17 4.44 4.54 2.75 3.13 0.98 591078_4 2.27 2.64 3.39 4.56 4.61 2.76 3.13 0.97 60 1078_5 2.40 2.46 3.414.48 4.88 2.72 3.12 0.98 61 1078_6 2.75 5.90 2.75 3.11 0.98 62 1078_72.08 2.49 3.35 4.83 4.83 2.77 3.14 0.97 63 1078_8 2.28 2.53 2.73 4.334.59 2.75 3.10 0.98 64 1078_9 2.21 2.49 3.11 4.31 4.77 2.74 3.11 0.98 651145_A 4.89 4.48 3.28 4.42 4.42 3.54 66 1145_B 4.89 4.48 3.28 4.42 4.423.54 67 1050 4.58 4.38 3.01 4.10 4.29 3.47 68 1253 4.38 3.69 3.39 4.363.83 2.87 1.37 69 1257 4.43 3.84 3.61 4.45 4.03 2.87 1.35 70 1297_1 4.313.81 3.46 4.35 3.86 2.87 1.39 71 1297_2 4.41 3.62 3.57 4.48 3.69 2.881.37 72 1297_3 4.37 3.85 3.55 4.43 3.92 2.85 1.39 73 1297_4 4.35 3.673.50 4.44 3.67 2.87 1.37 74 1297_5 4.56 3.82 3.43 4.59 3.88 2.86 1.38 751297_6 4.65 4.26 3.53 4.73 4.23 2.86 1.38 76 1304 4.40 3.85 3.37 4.393.89 2.84 1.38 77 1306_1 4.25 5.09 3.06 4.38 4.22 3.54 78 1306_2 6.075.71 2.68 3.99 4.29 3.60 79 1307 3.15 3.80 3.17 4.60 4.57 2.74 3.13 0.9880 1328_1 4.21 3.54 3.13 4.24 3.54 2.85 1.37 81 1328_2 4.38 3.84 3.084.43 4.01 2.85 1.38 82 1328_3 3.99 2.55 3.40 4.82 3.89 2.85 1.38 831328_4 4.21 2.53 3.71 5.05 3.83 2.85 1.37 84 1334 3.14 3.74 3.24 5.334.84 1.75 3.47 85 1335 4.68 3.12 5.11 6.60 4.33 3.55 86 1338 4.33 3.753.35 4.35 3.80 2.88 1.37 87 1345_1 4.08 3.57 3.48 4.52 4.49 88 1345_24.97 4.32 3.32 4.58 4.16 89 1351 4.47 3.70 3.38 4.47 3.79 2.85 1.38 901353 4.38 3.72 3.27 4.38 3.79 2.85 1.36 91 1360 4.38 3.80 3.32 4.35 3.852.85 1.36 92 1367 4.37 5.63 4.72 4.35 5.37 2.85 1.39 93 1368 4.34 8.847.07 4.30 8.92 2.86 1.39 94 1371 3.13 3.66 3.25 3.46 3.72 95 1372_A 4.403.88 3.32 4.38 3.94 2.85 1.38 96 1372_B 4.39 3.91 3.35 4.37 4.00 2.851.38 97 1373 4.40 3.78 3.38 4.41 3.86 2.85 1.37 98 1492 3.14 5.11 3.183.43 1.13 4.66 6.47 1.85 99 1399 4.40 3.82 3.33 4.40 3.92 2.86 1.38 1001406 4.35 3.89 3.29 4.36 4.00 2.86 1.38 101 1411 4.34 3.90 3.50 4.374.05 2.87 1.34 102 1433 3.16 3.59 3.46 5.49 4.76 1.77 3.47 103 1435 4.373.79 3.37 4.36 3.86 2.85 1.38 104 1441 4.29 3.79 3.29 4.27 3.96 2.851.37 105 1450_A 3.16 3.57 3.11 5.47 4.73 1.75 3.55 106 1450_B 3.14 3.463.83 5.49 4.57 1.74 3.41 average distance 3.98 3.97 3.59 5.08 3.80 4.704.52 3.46 2.86 1.37 2.59 3.17 0.97 standard deviation 1.07 1.13 1.031.78 2.48 0.65 0.95 0.43 0.01 0.01 0.37 0.13 0.01 minimum value 2.082.42 2.29 2.73 1.13 3.35 3.51 1.85 2.84 1.34 1.74 3.08 0.96 maximumvalue 6.97 8.84 9.57 7.04 8.45 7.59 9.42 3.66 2.88 1.39 2.84 3.55 0.98sample size 105 105 104 5 5 105 105 31 27 37 25 27 21 Table A5-2:Pharmacophore distance Pharmacophore Region S3 Region S4 Region elementsd(O2, d(O2, d(N2, d(N2, d(CA5, d(N2, d(N2, d(N2, d(N2, d(N2, d(N2, H3)N2) C2) C4) N2) CA2) C4)4 C6) CA3) O3) H1) 1 14 2 999_1 5.38 2.64 2.93 3999_2_A 5.47 2.40 3.23 4 999_2_B 5.15 2.58 3.00 5 1129 2.83 3.19 2.765.54 6 1034 2.74 3.03 2.26 3.72 7 1024 5.45 2.78 6.19 8 1042_1 5.43 2.643.42 6.20 9 1042_2 5.89 2.86 4.38 7.44 10 1042_3 6.75 4.11 3.55 6.60 112018 9.00 12 1059 4.97 2.67 3.70 5.88 13 1088_A 3.72 2.73 3.41 5.30 141088_B 3.82 2.68 3.90 6.13 15 1036_1 6.25 2.67 5.05 16 1036_2_1 5.472.80 5.11 17 1036_2_2 6.42 2.84 5.14 18 1081 5.78 2.76 7.56 6.05 7.56 191063 4.92 3.36 1.38 5.62 20 1065 4.40 2.83 1.40 5.75 21 1030_A 3.36 221030_B 3.28 23 1037 3.99 24 1118 5.85 2.67 7.40 5.84 7.40 8.27 25 10905.87 2.72 5.09 7.94 26 1007_1 4.41 2.79 6.02 27 1007_2 4.67 2.86 6.11 281149 5.29 4.42 7.94 29 1021_A 2.83 2.71 4.69 30 1021_B 2.30 2.65 5.22 311097_1 4.58 2.81 1.42 4.50 32 1097_2 4.29 2.81 1.42 4.50 33 1031_1 2.993.03 6.25 34 1031_2 3.09 3.00 5.86 35 1031_3 3.21 3.22 5.84 36 1031_43.10 3.13 6.23 37 1153_A 2.71 2.88 8.34 6.18 3.78 7.78 38 1153_B 3.102.99 8.53 3.75 5.06 9.72 39 1025_1 3.35 2.94 1.35 5.67 40 1025_2 2.632.79 1.32 5.62 41 1025_3 2.66 2.64 1.34 5.66 42 1025_4 2.43 2.95 1.355.58 43 1025_5 2.78 2.68 1.32 5.61 44 1025_6 1.27 3.00 1.34 5.64 451089_A 5.94 2.66 5.10 46 1089_B 5.91 2.70 5.10 47 1012_1 4.08 2.65 5.0748 1012_2 4.07 2.78 5.10 49 1078_1 2.93 2.77 1.48 5.74 50 1078_10 1.972.74 1.48 5.72 51 1078_11 3.05 2.97 1.47 5.75 52 1078_12 2.85 2.84 1.455.74 53 1078_13 2.11 2.79 1.47 5.61 54 1078_14 2.58 2.77 1.45 5.69 551078_15 2.97 2.84 1.45 5.66 56 1078_16 2.96 2.90 1.49 5.80 57 1078_22.53 2.72 1.44 5.72 58 1078_3 2.05 2.79 1.45 5.70 59 1078_4 2.72 2.701.51 5.66 60 1078_5 3.24 2.95 1.45 5.65 61 1078_6 1.49 5.49 62 1078_73.26 3.04 1.47 5.74 63 1078_8 2.69 2.85 1.44 5.66 64 1078_9 3.06 2.891.46 5.71 65 1145_A 5.36 2.77 5.91 5.59 7.97 8.64 66 1145_B 5.36 2.775.91 5.59 7.97 8.68 67 1050 2.72 2.76 6.69 5.73 68 1253 2.04 2.70 1.465.74 69 1257 2.18 2.71 5.09 6.64 70 1297_1 4.23 2.71 1.44 5.68 71 1297_23.98 2.84 1.47 5.78 72 1297_3 4.22 2.72 1.43 5.64 73 1297_4 4.02 2.761.47 5.72 74 1297_5 4.06 2.67 1.43 5.69 75 1297_6 4.15 2.83 1.44 5.72 761304 4.37 2.62 5.96 77 1306_1 5.26 2.66 6.06 78 1306_2 4.46 2.71 6.15 791307 2.09 2.81 6.14 80 1328_1 4.20 2.79 8.09 5.88 8.09 81 1328_2 4.542.75 7.87 5.92 7.87 82 1328_3 4.77 2.77 7.95 6.00 7.95 83 1328_4 4.712.79 7.92 6.17 7.92 84 1334 2.99 2.77 6.09 85 1335 5.33 2.70 5.83 861338 4.29 2.74 6.05 87 1345_1 5.98 2.90 6.14 5.17 8.75 88 1345_2 5.512.87 5.98 5.15 8.73 89 1351 4.26 2.76 6.12 90 1353 4.10 2.69 1.45 6.5091 1360 4.32 2.66 5.07 8.32 92 1367 2.68 93 1368 7.79 4.30 4.47 6.36 941371 1.96 2.79 5.90 95 1372_A 2.30 2.66 6.06 5.99 6.06 96 1372_B 2.232.63 6.02 5.56 97 1373 4.31 2.65 6.60 6.03 98 1492 7.20 99 1399 4.092.67 5.96 100 1406 4.44 2.64 5.98 101 1411 4.13 2.68 1.46 5.72 102 14332.89 2.65 1.51 5.79 103 1435 4.33 2.62 8.24 6.00 8.24 7.51 104 1441 4.152.72 1.45 5.75 105 1450_A 2.31 2.81 5.88 106 1450_B 2.32 2.67 6.07average distance 3.99 2.83 2.22 7.67 4.94 5.91 7.67 6.99 5.06 8.49 8.66standard deviation 1.42 0.30 1.64 0.62 0.62 0.41 0.62 1.01 0.67 0.670.02 minimum value 1.27 2.40 1.32 6.06 3.72 5.06 6.06 5.56 3.78 7.788.64 maximum value 9.00 4.42 8.53 8.24 6.60 8.32 8.24 8.27 5.59 9.728.68 sample size 104.00 98 51 9 18 81 9 4 5 6 2

TABLE A6 Table A6-1 Pharmacophore angles Pharmacophore Region S1 RegionS2 Region Elements a(O1, a(O1, a(CA1, A(N1, a(C3, a(N1, a(O1, a(C5,a(O1, a(CA1, O2, H4) CA6, O2) O1, O2) CA1, O1) a) CA1, O1) CA1, O1) b)CA1, O4) CA1, O1) CA1, C7) O4, H2) 1  14 61.95 75.74 139.05 2 999_1154.32 127.44 159.37 3 999_2_A 156.25 133.11 156.55 4 999_2_B 156.16140.65 153.11 5 1129 137.67 111.77 164.78 6 1034 135.95 111.64 160.69 71024 128.26 109.78 163.32 8 1042_1 122.15 117.21 158.11 9 1042_2 128.91116.12 164.17 10 1042_3 11 2018 118.45 159.18 100.76 169.37 12 1059140.37 102.43 176.16 13 1088_A 149.95 99.08 14 1088_B 153.40 99.27 151036_1 129.34 113.86 162.74 16 1036_2_1 134.57 105.64 163.26 17 1036_2_2128.96 108.40 164.16 18 1081 138.44 108.25 163.55 19 1063 142.43 88.32167.99 20 1065 148.95 110.77 165.45 21 1030_A 141.50 76.43 109.09 221030_B 138.56 115.15 23 1037 128.21 108.98 162.36 24 1118 139.63 111.55162.73 25 1090 121.29 100.34 26 1007_1 113.31 107.37 174.46 27 1007_2113.36 107.55 174.22 28 1149 105.44 131.55 147.27 168.87 29 1021_A101.19 87.17 100.00 158.12 30 1021_B 127.69 111.61 159.75 31 1097_1125.81 112.80 162.99 32 1097_2 137.06 109.11 163.92 33 1031_1 116.9890.53 62.36 160.22 123.26 34 1031_2 120.91 130.70 51.33 162.16 126.02 351031_3 119.04 93.66 52.73 163.39 122.20 36 1031_4 116.96 84.57 55.13161.31 122.41 37 1153_A 132.39 99.83 174.13 38 1153_B 92.62 144.91171.50 39 1025_1 125.08 118.04 171.14 40 1025_2 113.88 111.48 171.54 411025_3 117.96 107.75 174.66 42 1025_4 142.08 72.65 171.39 43 1025_5120.99 112.95 174.47 44 1025_6 104.02 106.08 170.14 45 1089_A 122.1698.23 46 1089_B 122.31 99.20 47 1012_1 129.53 107.17 173.56 48 1012_290.89 105.03 161.82 49 1078_1 103.21 111.94 68.03 160.22 126.79 501078_10 131.53 108.49 71.55 160.63 127.01 51 1078_11 88.73 109.94 59.87161.80 130.34 52 1078_12 128.90 111.74 67.44 161.92 127.55 53 1078_13123.59 115.77 65.06 162.99 129.33 54 1078_14 109.80 109.29 70.42 159.36126.58 55 1078_15 110.90 108.62 65.89 160.41 127.31 56 1078_16 101.76112.44 67.40 161.46 126.68 57 1078_2 91.16 109.26 65.74 159.94 128.74 581078_3 124.44 112.44 67.41 162.08 128.44 59 1078_4 93.17 112.48 65.56161.60 128.57 60 1078_5 90.82 117.54 55.67 164.79 131.80 61 1078_6 67.49152.72 126.69 62 1078_7 86.28 110.36 67.29 158.86 126.10 63 1078_8111.09 112.99 73.28 159.05 125.48 64 1078_9 97.24 117.85 66.67 161.68128.05 65 1145_A 139.31 111.73 162.28 66 1145_B 139.31 111.73 162.28 671050 140.76 114.34 160.78 68 1253 131.28 105.84 149.95 174.19 69 1257128.83 109.00 150.46 174.64 70 1297_1 130.08 107.14 149.59 174.57 711297_2 128.26 103.93 150.01 174.54 72 1297_3 129.38 107.42 150.32 174.7873 1297_4 129.06 103.60 149.60 174.41 74 1297_5 132.64 102.43 150.41174.11 75 1297_6 133.61 105.49 150.35 173.49 76 1304 132.43 105.87149.82 173.92 77 1306_1 143.05 107.94 158.44 78 1306_2 153.92 114.80161.00 79 1307 126.83 109.57 66.49 161.35 121.00 127.11 80 1328_1 133.34101.20 150.62 175.41 81 1328_2 136.71 103.89 150.10 173.89 82 1328_3122.23 97.62 150.74 173.57 83 1328_4 119.12 96.00 151.05 173.49 84 1334124.74 100.10 68.25 150.49 85 1335 100.88 91.76 170.77 86 1338 131.78105.30 148.99 173.72 87 1345_1 126.38 112.39 88 1345_2 138.87 105.43 891351 132.32 103.11 149.86 173.60 90 1353 133.22 103.61 149.99 173.73 911360 132.69 105.67 150.18 174.23 92 1367 125.36 129.48 149.67 173.97 931368 127.75 151.69 149.59 173.57 94 1371 123.31 121.03 95 1372_A 133.23106.33 149.88 174.16 96 1372_B 132.88 107.52 149.88 174.13 97 1373131.90 105.28 149.81 174.08 98 1492 143.64 87.17 137.45 173.84 99 1399132.84 105.80 149.86 173.87 100 1406 133.28 107.31 149.47 173.92 1011411 130.04 109.85 149.02 173.43 102 1433 118.66 97.80 65.77 151.25 1031435 131.96 106.19 149.49 173.74 104 1441 132.47 108.56 148.89 173.13105 1450_A 125.38 94.14 68.80 150.97 136.18 106 1450_B 109.15 98.9266.73 150.20 139.92 average distance 125.22 102.87 109.45 164.29 149.91173.40 64.89 159.21 132.37 126.98 standard deviation 16.57 31.42 12.065.24 0.51 2.19 5.55 4.12 8.18 2.30 minimum value 61.95 75.74 72.65153.11 148.89 161.82 51.33 150.20 121.00 122.20 maximum value 156.25159.18 151.69 176.16 151.05 175.41 73.28 164.79 139.92 131.80 samplesize 104 6 104 30 27 37 25 27 3 21 Table A6-2 Pharmacophore AnglePharmacophore Region S3 Region S4 Region RM Region Elements a(O1, a(O1,a(O2, a(O2, a(O2, a(O2, a(O2, a(O2, a(O2, a(O2, O2, H3) O2, N2) N2, C2)N2, C4) N2, CA2) N2, C4) 2 N2, C6) N2, CA3) N2, O3) N2, H1) 1  14 2 999_1 158.16 168.00 125.23 3  999_2_A 157.15 164.18 134.23 4  999_2_B152.90 175.07 127.87 5 1129 122.63 127.76 110.31 6 1034 135.88 137.69100.68 7 1024 151.79 136.56 154.55 8 1042_1 149.96 170.80 140.47 155.509 1042_2 152.56 148.96 139.99 158.67 10 1042_3 129.44 145.75 11 2018154.86 12 1059 148.70 132.46 139.14 153.47 13 1088_A 144.04 141.09141.58 14 1088_B 144.52 135.22 140.65 154.54 15 1036_1 153.49 143.79 161036_2_1 153.56 149.24 17 1036_2_2 154.60 146.84 18 1081 153.00 139.53161.57 153.98 119.80 19 1063 157.64 139.49 118.75 154.05 20 1065 145.76144.81 124.85 154.55 21 1030_A 146.48 22 1030_B 142.99 23 1037 145.74 241118 152.79 137.47 162.84 154.60 125.21 88.59 25 1090 152.05 140.84 261007_1 146.43 138.95 154.71 27 1007_2 145.74 133.10 153.46 28 1149 54.8862.73 154.82 49.80 29 1021_A 141.44 142.62 30 1021_B 140.90 147.46155.32 31 1097_1 152.91 134.93 125.76 32 1097_2 153.30 137.12 128.45 331031_1 123.16 130.39 153.37 34 1031_2 132.76 133.59 150.67 35 1031_3128.81 134.55 152.13 36 1031_4 124.03 130.34 152.78 37 1153_A 138.79132.96 168.69 152.46 157.3814094 167.70665 38 1153_B 25.95 44.76 163.28150.51 165.2913429 39 1025_1 129.17 125.11 132.16 158.42 40 1025_2137.62 130.51 139.00 161.47 41 1025_3 141.10 134.33 141.57 163.85 421025_4 170.92 162.26 126.70 154.93 43 1025_5 137.39 135.64 140.45 163.6144 1025_6 108.29 105.09 124.73 154.93 45 1089_A 153.00 141.72 154.37 461089_B 152.83 141.07 47 1012_1 144.24 141.07 48 1012_2 141.64 140.42 491078_1 141.96 145.93 121.70 154.68 50 1078_10 146.00 152.80 131.78156.19 51 1078_11 137.81 142.32 120.15 152.82 52 1078_12 150.80 154.56130.32 157.60 53 1078_13 135.66 146.15 127.57 154.39 54 1078_14 144.55148.03 129.57 155.65 55 1078_15 143.22 147.42 124.17 155.02 56 1078_16140.06 144.54 122.62 154.31 57 1078_2 141.98 146.00 128.07 155.89 581078_3 132.07 145.54 126.01 154.83 59 1078_4 141.42 146.07 126.96 155.5460 1078_5 138.56 141.15 114.27 151.79 61 1078_6 62 1078_7 137.32 140.50114.22 151.33 63 1078_8 140.66 145.13 125.44 153.81 64 1078_9 142.04146.14 119.45 153.36 65 1145_A 150.25 136.24 153.28 161.48 168.41 168.8166 1145_B 150.25 136.24 153.28 161.48 168.41 168.66 67 1050 137.51140.97 159.29 153.66 68 1253 134.57 140.99 130.77 155.92 69 1257 132.63141.45 105.30 70 1297_1 144.22 143.88 130.88 156.06 71 1297_2 144.48141.45 127.48 154.79 72 1297_3 143.41 144.44 132.31 156.50 73 1297_4145.24 143.80 131.10 156.08 74 1297_5 146.79 147.10 132.77 157.05 751297_6 144.79 141.32 116.76 154.05 76 1304 147.16 139.74 156.83 771306_1 152.11 135.46 155.89 78 1306_2 151.24 153.80 158.08 79 1307129.22 142.81 155.37 80 1328_1 150.01 145.32 161.66 155.25 114.03 811328_2 149.68 139.05 160.74 154.85 109.44 82 1328_3 151.35 139.67 160.41154.95 106.08 83 1328_4 150.66 142.82 160.57 156.25 109.36 84 1334136.63 143.82 155.99 85 1335 152.03 130.91 154.21 86 1338 148.03 141.48157.11 87 1345_1 149.79 134.33 153.15 153.91 163.54 88 1345_2 152.27142.63 153.90 151.66 162.76 89 1351 148.60 141.59 158.04 90 1353 146.74137.66 130.69 157.19 91 1360 147.57 138.89 162.09 92 1367 107.78 93 1368119.72 74.03 145.05 94 1371 136.64 146.93 155.86 95 1372_A 137.15 140.15159.60 155.91 127.51 96 1372_B 139.74 143.19 157.88 115.79 97 1373147.32 141.07 156.78 98 1492 153.97 99 1399 145.77 143.45 157.06 1001406 147.38 140.17 156.30 101 1411 142.75 140.47 130.32 155.94 102 1433135.90 141.60 129.89 155.75 103 1435 147.24 139.75 164.21 157.86 121.0699.38 104 1441 145.43 144.23 131.10 156.32 105 1450_A 127.40 139.62154.51 106 1450_B 123.50 138.89 155.81 average distance 141.41 139.32130.19 160.71 155.18 109.14 102.26 157.18 166.02 168.74 standarddeviation 17.50 16.79 11.79 2.46 2.86 22.13 9.84 3.95 2.29 0.08 minimumvalue 25.95 44.76 100.68 154.82 145.05 49.80 88.59 151.66 162.76 168.66maximum value 170.92 175.07 168.69 164.21 163.85 127.51 115.79 161.48168.41 168.81 sample size 103 97 97 9 80 9 4 5 6 2 Footnote: a) Allcompounds with protonatable center N1 except Methyl-amino-pyridine b)Methyl-amino-pyridine compounds

TABLE A7 Table A7-1 Pharmacophore torsion Angles Pharmacophore Region S2Region S1 Region S3 Region elements a(O1, a(N1, a(C3, a(N1, a(C5, a(C7,a(H4, a(H4, a(O1, a(CA6, O1, H4, CA1, CA1, CA1, CA1, CA1, O1, O1, O2,a(O1, O2, H4, O2) O2, CA1) O2, H4) O1, H4) O1, H4) O1, H4) O1, H4) O2,H3) O2, N2) N2, C2) N2, C2)2 1  14 43.29 38.29 2 999_1 −126.77 −136.6321.52 126.59 95.00 95.00 3 999_2_A −126.58 −134.62 20.92 107.88 109.28109.28 4 999_2_B −154.08 −159.59 12.97 142.07 73.39 73.39 5 1129 −65.27−139.56 104.70 133.45 95.54 95.54 6 1034 −61.32 −127.27 93.33 142.8368.39 68.39 7 1024 −63.40 −97.21 44.69 125.09 8 1042_1 −160.50 9.10−19.99 68.67 115.48 115.48 9 1042_2 68.80 69.40 −9.33 44.33 151.54151.54 10 1042_3 11 2018 −9.94 −146.71 −154.72 30.27 12 1059 −89.48−131.19 47.74 121.97 129.30 129.30 13 1088_A −54.60 49.33 120.82 103.40103.40 14 1088_B −63.34 45.99 121.15 129.99 129.99 15 1036_1 −63.13−93.66 32.81 124.11 16 1036_2_1 −44.90 −89.39 41.52 133.12 17 1036_2_2−56.75 −100.27 33.33 119.08 18 1081 −62.03 −125.05 36.36 121.47 19 1063−74.94 −130.71 54.13 155.02 150.29 150.29 20 1065 −21.94 −89.34 44.38129.83 124.96 124.96 21 1030_A 18.23 −63.68 52.95 22 1030_B −59.93 53.9923 1037 −51.12 −92.49 57.29 24 1118 −65.17 −132.91 38.74 128.20 25 1090−92.71 91.31 −177.46 26 1007_1 −94.99 39.07 50.93 137.94 27 1007_2−94.30 48.80 47.32 126.25 28 1149 55.30 −48.11 −109.82 105.58 125.02 291021_A −66.24 32.57 −132.46 −124.87 30 1021_B −86.96 −13.44 −171.75−168.95 31 1097_1 −66.34 −97.71 86.65 121.05 136.92 136.92 32 1097_2−71.28 −142.69 91.00 129.42 125.27 125.27 33 1031_1 −175.07 −101.95142.57 137.86 34 1031_2 −138.43 36.72 63.49 56.56 35 1031_3 −164.95−92.95 149.50 144.29 36 1031_4 −175.49 −110.81 138.85 134.30 37 1153_A15.20 −11.60 86.11 97.90 30.40 30.40 38 1153_B 23.08 56.56 70.64 133.70−139.94 −139.94 39 1025_1 −141.34 6.68 −40.49 −77.23 −47.33 −47.33 401025_2 −163.82 −28.78 −54.10 −98.22 −27.27 −27.27 41 1025_3 139.58−15.01 −52.28 −100.26 −32.71 −32.71 42 1025_4 150.81 −85.37 127.24161.32 45.78 45.78 43 1025_5 −169.75 −23.34 −32.05 −85.30 −34.65 −34.6544 1025_6 −135.64 −7.52 122.08 166.26 88.55 88.55 45 1089_A −95.88 88.95−175.67 46 1089_B −94.63 89.27 −178.39 47 1012_1 −84.31 10.25 50.86137.94 48 1012_2 −50.19 −107.13 162.80 −124.02 49 1078_1 −60.12 25.08−119.94 −112.97 138.25 138.25 50 1078_10 −84.11 −9.97 −152.67 −164.78123.40 123.40 51 1078_11 −55.96 37.14 −120.02 −112.40 136.21 136.21 521078_12 −75.33 11.21 −120.32 −108.09 114.97 114.97 53 1078_13 −78.80−7.66 −157.30 −162.99 118.91 118.91 54 1078_14 −62.09 20.44 −134.39−121.21 126.74 126.74 55 1078_15 −64.96 19.98 −124.63 −117.88 139.14139.34 56 1078_16 −58.07 14.30 −119.50 −111.94 136.30 136.30 57 1078_2−57.88 38.04 −132.87 −119.25 127.17 127.17 58 1078_3 −82.33 −5.62−160.53 −166.69 132.95 132.95 59 1078_4 −58.33 32.90 −123.98 −113.42124.98 124.98 60 1078_5 −52.04 21.83 −119.72 −115.76 148.01 148.01 611078_6 −22.50 62 1078_7 −57.85 30.48 −121.10 −116.26 144.61 144.61 631078_8 −58.50 5.11 −134.33 −122.87 135.84 135.84 64 1078_9 −50.72 14.92−116.62 −110.81 144.64 144.64 65 1145_A −59.90 −128.41 48.71 124.15 661145_B −59.90 −128.41 48.71 124.15 67 1050 −58.32 −131.38 102.21 123.4566.94 66.94 68 1253 −82.09 26.20 3.75 115.64 140.24 120.69 120.69 691257 −83.51 30.77 11.94 108.60 132.94 70 1297_1 −85.98 30.15 26.85 50.42137.09 117.40 117.40 71 1297_2 −87.24 29.10 23.27 51.75 141.21 116.16116.16 72 1297_3 −86.03 28.95 22.83 50.29 141.16 114.36 114.36 73 1297_4−89.51 28.23 26.25 51.40 142.36 110.29 110.29 74 1297_5 −86.41 30.1210.41 47.86 144.38 111.81 111.81 75 1297_6 −89.84 27.46 5.20 43.22150.19 132.97 132.97 76 1304 −84.58 24.93 5.90 49.79 138.09 77 1306_1−170.32 106.51 36.21 120.80 78 1306_2 −12.97 −77.87 40.51 134.08 79 1307−88.47 −6.78 −161.01 −163.22 −170.13 80 1328_1 −88.07 30.10 20.31 55.62136.65 81 1328_2 −83.32 21.76 −4.36 51.26 134.72 82 1328_3 −87.28 57.5239.33 47.98 130.71 83 1328_4 −91.48 66.00 58.16 44.95 135.08 84 1334−93.67 2.51 110.57 −172.73 85 1335 −127.40 −112.46 55.79 140.77 86 1338−85.13 23.02 −3.32 52.11 140.39 87 1345_1 −62.84 39.71 114.36 88 1345_2−68.67 49.59 128.64 89 1351 −83.97 26.55 −0.13 51.88 138.69 90 1353−84.72 23.38 3.14 51.34 136.30 126.15 126.15 91 1360 −83.81 24.01 3.3451.00 138.89 92 1367 −85.54 23.21 1.25 42.45 93 1368 −74.89 22.95 −2.2640.86 68.19 94 1371 −68.15 −165.12 −174.11 95 1372_A −83.68 25.78 5.7399.84 136.36 96 1372_B −82.66 25.77 4.96 99.85 139.62 97 1373 −84.4225.67 4.28 50.98 139.02 98 1492 −19.90 −60.21 −132.36 94.72 99 1399−83.35 24.20 0.87 50.25 142.63 100 1406 −83.05 23.93 −2.51 50.99 135.75101 1411 −82.11 24.51 −2.21 55.16 137.13 117.46 117.46 102 1433 −96.266.40 109.26 −171.69 118.46 118.46 103 1435 −83.48 24.44 1.43 51.39136.22 104 1441 −80.01 21.88 −6.82 50.54 141.99 117.29 117.29 105 3450_A−99.46 −8.42 −160.66 −165.58 −172.83 106 1450_B −91.88 13.21 −150.35−176.95 177.59 average distance 17.40 −76.06 −92.19 28.54 2.57 −0.88−157.34 17.93 47.94 99.05 99.05 standard deviation 29.14 50.45 67.169.82 29.67 39.57 4.95 88.16 124.93 59.50 59.50 minimum value −19.90−175.49 −159.59 21.76 −107.13 −110.81 −161.01 −176.95 −178.39 −139.94−139.94 maximum value 55.30 150.81 106.51 66.00 58.16 38.04 −150.35162.80 177.59 151.54 151.54 sample size 5 104 30 27 37 27 3 103 97 49 49Table A7-2 Pharmacophore torsion angles Pharmacophore Region S4 RegionRM Region Elements a(O1, a(O1, a(O1, a(O1, a(O2, a(O1, a(O1, O2, a(O1,O2, O2, N2, CA5) O2, N2, CA2) O2, N2, CA4) O2, N2, C6) N2, CA2) O2, N2,O3) N2, H1) N2, CA3) 1  14 2 999_1 3 999_2_A 4 999_2_B 5 1129 145.95 61034 137.68 7 1024 139.71 154.55 8 1042_1 136.01 155.50 9 1042_2 159.77158.67 10 1042_3 145.75 11 2018 12 1059 134.69 153.47 13 1088_A 116.2714 1088_B 134.51 154.54 15 1036_1 142.62 16 1036_2_1 136.82 17 1036_2_2137.32 18 1081 142.86 153.98 19 3063 133.32 154.05 20 1065 129.88 154.5521 1030_A 22 1030_B 23 1037 24 1118 145.00 150.07 154.60 25 1090 134.9126 1007_1 128.23 154.71 27 1007_2 131.44 153.46 28 1149 155.91 29 1021_A94.53 30 1021_B 136.58 155.32 31 1097_1 148.15 32 1097_2 137.08 331031_1 124.94 153.37 34 1031_2 457.89 150.67 35 1031_3 133.88 152.13 361031_4 127.07 152.78 37 1153_A 116.41 152.46 43.95 24.87 38 1153_B−161.98 76.90 150.51 −144.09 39 1025_1 −46.36 158.42 40 1025_2 −25.28161.47 41 1025_3 −34.46 163.85 42 1025_4 44.29 154.93 43 1025_5 −36.22163.61 44 1025_6 87.30 154.93 45 1089_A 137.41 154.37 46 1089_B 133.3847 1012_1 127.02 48 1012_2 133.17 49 1078_1 140.46 154.68 50 1078_10136.18 156.19 51 1078_11 138.54 152.82 52 1078_12 110.39 157.60 531078_13 137.37 154.39 54 1078_14 134.23 155.65 55 1078_15 141.63 155.0256 1078_16 139 28 154.31 57 1078_2 137.47 155.89 58 1078_3 140.71 154.8359 1078_4 136.93 155.54 60 1078_5 149.21 151.79 61 1078_6 62 1078_7143.84 151.33 63 1078_8 143.43 153.81 64 1078_9 146.06 153.36 65 1145_A140.87 153.28 −10.98 −17.10 −15.65 66 1145_B 140.87 153.28 −10.98 −15.97−15.65 67 1050 147.29 153.66 68 1253 126.24 155.92 69 1257 134.25 146.1370 1297_1 131.38 110.58 156.06 71 1297_2 126.84 106.20 154.79 72 1297_3129.56 108.64 156.50 73 1297_4 126.11 105.94 156.08 74 1297_5 122.50101.00 157.05 75 1297_6 131.04 109.63 154.05 76 1304 125.90 156.83 771306_1 136.58 155.89 78 1306_2 124.98 158.08 79 1307 138.35 155.37 801328_1 126.19 155.25 81 1328_2 132.29 154.85 82 1328_3 131.79 154.95 831328_4 128.70 156.25 84 1334 133.84 155.99 85 1335 118.45 154.21 86 1338124.64 116.54 157.11 87 1345_1 138.94 153.15 −11.99 −27.29 88 1345_2129.85 153.90 −20.78 −34.52 89 1351 121.52 119.61 158.04 90 1353 120.30157.19 91 1360 129.35 130.24 162.09 92 1367 93 1368 124.36 −100.57145.05 94 1371 136.54 155.86 95 1372_A 129.48 155.91 96 1372_B 109.73141.41 157.88 97 1373 91.76 127.58 156.78 98 1492 99 1399 126.87 113.10157.06 100 1406 127.54 102.90 156.30 101 1411 127.52 155.94 102 1433127.94 155.75 103 1435 123.48 137.30 157.86 104 1441 126.16 156.32 1051450_A 120.74 154.51 106 1450_B 137.59 155.81 average distance 113.48114.59 113.64 143.73 155.18 −25.81 −16.54 −13.65 standard deviation68.44 56.45 14.37 4.82 2.89 57.03 0.57 20.56 minimum value −161.98−157.89 101.00 137.30 145.05 −144.09 −17.10 −34.52 maximum value 148.15159.77 155.91 150.07 163.85 43.95 −15.97 24.87 sample size 18 79 11 4 806 2 5

TABLE A8 Table A8-1 Pharmacophore Protein distance Pharmacophore elementH4 O2 CA6 C3 protein TRP_655 SER_633 HIS_483 SER_654 GLY_656 TRP_655PHE_529 CYS_629 SER_628 VAL_653 TRP_655 1  14 HA 2.47 HE1 2.86 O 2.46 H2.53 HB2 2.82 HZ 2.99 O 3.64 HB2 3.26 HG12 2.83 HA 3.56 2 54_A HA 2.52HG 2.62 HE1 3.37 O 2.47 H 2.64 HB2 2.67 HZ 3.05 O 3.54 HB2 3.40 HG122.74 HA 3.49 3 54_B HA 2.52 OG 2.71 HE1 3.37 O 2.47 H 2.64 HB2 2.67 HZ3.05 O 3.54 HB2 3.40 HG12 2.74 HA 3.49 4 1129 HA 2.51 HG 2.83 HE1 3.47 O2.47 H 2.13 HA 2.99 HZ 3.41 O 3.35 HG 3.42 HG13 2.71 HA 3.97 5 1034 HA2.65 HG 2.58 NE2 3.42 O 2.38 H 2.36 HA 2.95 HZ 3.60 HA 3.14 OG 3.64 HG122.61 HA 4.08 6 1024 HA 2.61 HG 3.11 NE2 3.44 O 2.40 H 2.24 HB2 2.82 HZ3.53 O 3.55 HG 3.21 HG12 2.71 HA 3.82 7 1042_1 HA 2.73 HG 2.65 HE1 3.09O 2.37 H 2.70 HB2 3.15 HZ 4.53 H 3.31 HB2 2.80 HG11 2.67 HA 3.39 81042_2 HA 2.72 HG 3.87 HE1 3.73 O 2.79 H 2.65 HB2 3.10 HZ 3.24 HA 3.29HB2 3.71 HG11 3.04 HA 3.67 9 1042_3 HA 3.26 HG 2.70 HE2 2.63 O 2.57 H2.94 HA 2.93 HZ 3.22 HA 3.33 HB2 2.73 HG11 1.96 HA 4.22 10 2018 HA 2.70OG 2.80 HE2 2.92 O 2.35 H 2.45 HB2 2.92 HZ 2.96 O 3.55 HB2 3.40 HG122.68 HA 3.78 11 1059 HA 2.60 OG 3.18 HE1 3.16 O 2.22 H 2.39 HB2 2.82 HZ3.38 HA 3.59 OG 3.91 HG13 2.81 HA 3.77 12 1088_A HA 2.57 HG 3.34 NE23.59 O 2.31 H 2.29 HB2 2.85 HZ 3.50 O 3.66 OG 3.94 HG13 2.77 HA 3.81 131088_B HA 2.57 HG 3.31 NE2 3.59 O 2.31 H 2.29 HB2 2.85 HZ 3.50 O 3.66 OG3.94 HG13 2.77 HA 3.81 14 1036_1 HA 2.50 HG 3.07 HE1 3.49 O 2.32 H 2.14HB2 2.82 HZ 3.24 O 3.70 HB2 3.21 HG12 2.60 HA 3.84 15 1036_2_1 HA 2.59OG 3.43 HE1 2.60 O 2.32 H 2.64 HB2 2.82 HZ 3.00 O 3.78 HG 3.48 HG13 2.72HA 3.81 16 1036_2_2 HA 2.50 HG 3.12 HE1 3.86 O 2.50 H 2.23 HB2 2.68 HZ3.12 O 3.28 OG 3.72 HG12 2.66 HA 3.57 17 1081 HA 2.72 OG 3.67 HE2 3.39 O2.26 H 2.47 HB2 2.87 HZ 3.32 O 3.56 OG 3.74 HG13 2.61 HA 3.77 18 1063 HA2.65 HG 3.27 HE1 3.62 O 2.30 H 2.39 HB2 2.74 HZ 3.29 O 3.73 HG 3.36 HG132.52 HA 3.72 19 1065 HA 2.52 HG 3.30 NE2 3.54 O 2.32 H 2.36 HB2 2.73 HZ3.17 O 3.71 OG 3.46 HG13 2.57 HA 3.67 20 1030_A HA 2.50 OG 3.23 HE1 3.18O 2.26 H 2.27 HB2 2.88 HZ 3.32 O 3.73 HB2 3.19 HG13 2.58 HA 3.87 211030_B HA 2.50 OG 3.23 HE1 3.18 O 2.26 H 2.27 HB2 2.88 HZ 3.32 O 3.73HB2 3.19 HG13 2.58 HA 3.87 22 1037 HA 2.46 HG 2.93 NE2 3.86 O 2.26 H2.44 HB2 2.67 HZ 3.17 O 3.33 HB3 3.70 HG13 2.62 HA 3.71 23 1118 HA 2.60HG 3.29 NE2 3.67 O 2.52 H 2.22 HA 2.94 HZ 3.57 O 3.65 HB2 3.03 HG13 2.55HA 4.01 24 1090 HA 2.56 HG 2.81 HE1 3.32 O 2.19 H 2.26 HB2 2.67 HZ 3.06HA 3.62 OG 4.05 HG12 2.57 HA 3.71 25 1007_1 HA 2.35 HG 3.50 HE1 3.77 O2.45 H 2.30 HB2 2.69 HZ 3.18 O 3.43 O 3.15 HG13 2.77 HA 3.46 26 1007_2HA 2.41 OG 3.64 HE2 3.45 O 2.25 H 2.45 HB2 2.61 HZ 3.20 O 3.63 O 3.65HG13 2.76 HA 3.39 27 1149 HA 2.51 OG 3.42 HE2 2.91 O 2.14 H 2.79 HB22.71 HZ 3.69 O 3.35 OG 3.58 HG12 2.84 HA 3.65 28 1021_A HA 2.60 OG 3.35HE2 3.09 O 2.31 H 2.48 HB2 2.82 HZ 2.97 O 3.74 HB2 3.38 HG12 2.87 HA3.64 29 1021_B HA 2.59 OG 3.35 HE2 3.09 O 2.30 H 2.47 HB2 2.82 HZ 2.97 O3.75 HB2 3.38 HG12 2.87 HA 3.64 30 1097_1 HA 2.66 OG 3.29 HE2 3.33 O2.34 H 2.32 HB2 2.90 HZ 3.38 O 3.44 HG 3.36 HG13 2.73 HA 3.91 31 1097_2HA 2.63 OG 3.22 HE2 3.32 O 2.31 H 2.17 HB2 2.81 HZ 3.38 O 3.55 HG 3.34HG13 2.76 HA 3.86 32 1031_1 HA 2.61 HG 3.13 NE2 3.48 O 2.43 H 2.51 HB22.73 HZ 3.24 O 3.85 HB3 3.29 HG13 2.71 HA 3.57 33 1031_2 HA 2.59 HG 3.14NE2 3.54 O 2.42 H 2.48 HB2 2.71 HZ 3.17 O 3.83 HB3 3.34 HG13 2.77 HA3.53 34 1031_3 HA 2.64 OG 3.56 HE2 3.19 O 2.49 H 2.50 HB2 2.81 HZ 3.25 O3.74 HB3 3.30 HG13 2.78 HA 3.63 35 1031_4 HA 2.61 HG 2.98 NE2 3.46 O2.47 H 2.49 HB2 2.76 HZ 3.28 O 3.74 HB3 3.31 HG13 2.78 HA 3.58 36 1153_AHA 2.62 HG 2.60 HE1 3.31 O 2.43 H 2.29 HB2 2.91 HZ 4.04 O 3.49 HG 3.30HG13 2.63 HA 3.93 37 1153_B HA 2.62 HG 2.59 HE1 3.31 O 2.43 H 2.29 HB22.91 HZ 4.04 O 3.49 HG 3.24 HG13 2.63 HA 3.93 38 1025_1 HA 2.80 HG 2.82HE2 3.29 O 2.27 H 2.57 HB2 2.95 HZ 3.38 O 3.70 HG 3.34 HG11 2.52 HA 3.7739 1025_2 HA 2.89 OG 3.45 HE2 3.18 O 2.47 H 2.79 HB2 3.08 HZ 3.24 O 3.70O 3.35 HG11 2.74 HA 3.71 40 1025_3 HA 2.61 OG 3.89 HE2 3.46 O 2.46 H2.45 HB2 2.72 HZ 3.05 O 3.79 HG 2.70 HG12 2.83 HA 3.55 41 1025_4 HA 2.55HG 3.33 NE2 3.68 O 2.28 H 2.72 HB2 2.86 HZ 3.28 O 3.16 O 3.36 HG11 2.83HA 3.75 42 1025_5 HA 2.72 HG 3.45 NE2 3.51 O 2.13 H 2.53 HB2 2.80 HZ2.94 HA 3.46 O 2.97 HG11 2.65 HA 3.63 43 1025_6 HA 2.78 HG 2.97 HE1 3.10O 2.22 H 2.91 HB2 2.71 HZ 3.18 O 3.67 HB2 3.35 HG12 2.75 HA 3.37 441089_A HA 2.55 HG 2.97 HE1 3.32 O 2.23 H 2.24 HB2 2.73 HZ 3.35 O 3.61 OG4.12 HG12 2.72 HA 3.75 45 1089_B HA 2.55 HG 2.96 HE1 3.32 O 2.23 H 2.24HB2 2.73 HZ 3.35 O 3.61 OG 4.12 HG12 2.72 HA 3.75 46 1012_1 HA 2.64 HG3.23 HE1 3.40 O 2.35 H 2.49 HB2 2.74 HZ 3.07 O 3.84 HB2 3.35 HG13 2.65HA 3.62 47 1012_2 HA 2.37 HG 3.42 HE1 3.75 O 2.23 H 2.27 HB2 2.54 HZ3.13 O 3.89 OG 3.25 HG13 2.67 HA 3.58 48 1078_1 HA 2.51 HG 3.32 NE2 3.69O 2.43 H 2.41 HB2 2.75 HZ 3.10 HA 3.83 OG 3.80 HG13 2.88 HA 3.49 491078_10 HA 2.71 OG 3.45 HE2 3.15 O 2.48 H 2.53 HB2 2.89 HZ 3.20 HA 3.85HG 2.94 HG13 2.77 HA 3.60 50 1078_11 HA 2.50 OG 3.65 HE2 3.36 O 2.42 H2.40 HB2 2.76 HZ 3.03 HA 3.82 HG 2.96 HG13 2.88 HA 3.48 51 1078_12 HA2.47 HG 3.42 NE2 3.76 O 2.43 H 2.38 HB2 2.76 HZ 3.08 HA 3.80 HG 2.87HG13 2.90 HA 3.49 52 1078_13 HA 2.50 HG 3.39 NE2 3.69 O 2.42 H 2.37 HB22.76 HZ 3.07 HA 3.83 HG 2.87 HG13 2.87 HA 3.51 53 1078_14 HA 2.49 HG3.29 NE2 3.73 O 2.44 H 2.36 HB2 2.77 HZ 3.15 HA 3.79 HG 2.89 HG13 2.89HA 3.51 54 1078_15 HA 2.49 OG 3.64 HE2 3.38 O 2.45 H 2.39 HB2 2.77 HZ3.17 HA 3.80 HG 2.92 HG13 2.91 HA 3.49 55 1078_16 HA 2.47 OG 3.70 HE23.43 O 2.43 H 2.36 HB2 2.78 HZ 3.12 HA 3.83 HG 2.91 HG13 2.89 HA 3.50 561078_2 HA 2.47 HG 3.32 NE2 3.76 O 2.45 H 2.35 HB2 2.76 HZ 3.25 HA 3.80HG 2.88 HG13 2.87 HA 3.52 57 1078_3 HA 2.67 HG 3.18 NE2 3.59 O 2.47 H2.51 HB2 2.84 HZ 3.16 HA 3.77 HG 2.85 HG13 2.81 HA 3.59 58 1078_4 HA2.45 HG 3.36 NE2 3.77 O 2.44 H 2.35 HB2 2.75 HZ 3.13 HA 3.80 HG 2.85HG13 2.89 HA 3.49 59 1078_5 HA 2.48 HG 3.36 NE2 3.72 O 2.44 H 2.38 HB22.75 HZ 3.20 HA 3.80 HG 2.90 HG13 2.90 HA 3.49 60 1078_6 HA 2.50 HG 3.35NE2 3.72 O 2.46 H 2.38 HB2 2.78 HZ 3.14 HA 3.82 HG 2.91 HG13 2.90 HA3.51 61 1078_7 HA 2.51 HG 3.34 NE2 3.70 O 2.43 H 2.40 HB2 2.76 HZ 3.07HA 3.82 HG 2.88 HG13 2.88 HA 3.49 62 1078_8 HA 2.49 HG 3.32 NE2 3.71 O2.42 H 2.38 HB2 2.74 HZ 3.07 HA 3.84 HG 2.86 HG13 2.87 HA 3.48 63 1078_9HA 2.46 HG 3.41 NE2 3.78 O 2.44 H 2.37 HB2 2.77 HZ 3.11 HA 3.79 HG 2.84HG13 2.93 HA 3.48 64 1145_A HA 2.52 HG 3.11 HE1 3.76 O 2.40 H 2.20 HB22.83 HZ 3.75 O 3.54 HG 3.09 HG13 2.70 HA 3.83 65 1145_B HA 2.52 HG 3.10HE1 3.76 O 2.40 H 2.20 HB2 2.83 HZ 3.75 O 3.54 HG 3.08 HG13 2.70 HA 3.8366 1050 HA 2.50 OG 3.34 HE1 3.60 O 2.57 H 2.30 HB2 2.70 HZ 3.43 O 3.63HB2 3.34 HG13 2.66 HA 3.60 67 1253 HA 2.59 OG 3.04 HE1 3.01 O 2.09 H2.47 HB2 2.70 HZ 3.30 O 3.74 HB3 3.45 HG12 2.89 HA 3.56 68 1257 HA 2.49OG 3.16 HE1 3.21 O 2.15 H 2.28 HB2 2.65 HZ 3.23 O 3.72 HG 3.45 HG12 2.93HA 3.60 69 999_1 HA 2.59 HG 2.76 HE1 3.12 O 2.41 H 2.48 HB2 2.85 HZ 3.08HA 2.96 HB2 3.82 HG12 2.77 HA 3.75 70 999_2_A HA 2.50 HG 3.08 NE2 3.53 O2.51 H 2.48 HB2 2.87 HZ 3.44 O 3.32 HB2 3.58 HG13 2.65 HA 3.92 71999_2_B HA 2.50 HG 3.03 HE2 3.08 O 2.51 H 2.48 HB2 2.87 HZ 3.44 O 3.32HB2 3.58 HG13 2.65 HA 3.92 72 1297_1 HA 2.50 HG 2.82 HE1 3.61 O 2.07 H2.42 HB2 2.66 HZ 3.05 O 3.74 HB2 3.76 HG13 2.95 HA 3.42 73 1297_2 HA2.48 HG 2.85 HE1 3.63 O 2.06 H 2.38 HB2 2.63 HZ 3.01 O 3.78 HB2 3.12HG13 2.94 HA 3.42 74 1297_3 HA 2.55 OG 3.19 HE2 3.19 O 2.11 H 2.43 HB22.72 HZ 3.18 O 3.72 OG 3.70 HG13 2.92 HA 3.50 75 1297_4 HA 2.46 HG 2.90HE1 3.63 O 2.06 H 2.36 HB2 2.63 HZ 3.04 HA 3.78 HB2 3.12 HG13 2.95 HA3.42 76 1297_5 HA 2.52 HG 2.88 HE1 3.62 O 2.09 H 2.41 HB2 2.68 HZ 3.10HA 3.68 HG 3.46 HG13 2.95 HA 3.46 77 1297_6 HA 2.59 HG 2.82 NE2 3.62 O2.15 H 2.47 HB2 2.74 HZ 3.17 HA 3.65 HB2 3.69 HG13 2.92 HA 3.52 78 1304HA 2.59 OG 2.92 HE1 3.01 O 2.09 H 2.46 HB2 2.69 HZ 3.22 O 3.73 HB2 3.29HG12 2.83 HA 3.59 79 1306_1 HA 2.52 HG 2.70 HE2 3.08 O 2.04 H 2.08 HB22.36 HZ 2.88 O 3.38 OG 3.49 HG13 2.51 HA 3.80 80 1306_2 HA 2.50 HG 2.36HE1 3.23 O 2.16 H 2.22 HB2 2.36 HZ 2.59 O 3.32 OG 3.41 HG13 2.40 HA 3.7681 1307 HA 2.72 OG 2.90 HE2 3.07 O 2.22 H 2.64 HB2 2.74 HZ 2.56 O 3.81HB2 3.37 HG13 2.80 HA 3.54 82 1328_1 HA 2.48 HG 3.28 HE1 3.22 O 2.17 H2.55 HB2 2.63 HZ 3.13 HA 3.68 HB2 3.33 HG12 2.91 HA 3.38 83 1328_2 HA2.51 OG 3.21 HE1 3.27 O 2.19 H 2.58 HB2 2.69 HZ 3.05 O 3.65 HB2 3.10HG12 2.87 HA 3.40 84 1328_3 HA 2.43 HG 2.84 HE1 3.23 O 2.23 H 2.43 HB22.67 HZ 3.13 O 3.67 HB2 3.09 HG12 2.88 HA 3.49 85 1328_4 HA 2.49 HG 2.92HE1 3.22 O 2.19 H 2.43 HB2 2.68 HZ 3.17 O 3.70 HB2 3.03 HG12 2.83 HA3.52 86 1334 HA 2.70 OG 3.82 HE2 3.29 O 2.59 H 2.38 HB2 2.88 HZ 3.31 O3.77 HB2 3.52 HG13 2.60 HA 3.85 87 1335 HA 2.61 HG 3.26 HE1 3.62 O 2.38H 2.25 HA 2.84 HZ 3.47 O 3.65 HB2 3.30 HG13 2.53 HA 3.95 88 1338 HA 2.65HG 3.05 HE1 3.38 O 2.13 H 2.52 HB2 2.63 HZ 3.07 O 3.69 HB3 3.40 HG132.83 HA 3.54 89 1345_1 HA 2.32 HG 2.83 HE1 3.25 O 2.13 H 2.03 HB2 2.41HZ 2.79 O 3.50 HB2 3.31 HG12 2.77 HA 3.57 90 1345_2 HA 2.56 HG 2.99 HE13.59 O 2.43 H 2.24 HA 2.88 HZ 3.38 O 3.21 HB2 2.96 HG12 2.60 HA 3.86 911351 HA 2.59 HG 3.14 HE1 3.61 O 2.19 H 2.50 HB2 2.75 HZ 3.33 O 3.71 HB23.25 HG13 2.93 HA 3.60 92 1353 HA 2.59 OG 2.90 HE1 2.98 O 2.06 H 2.47HB2 2.58 HZ 3.20 O 3.71 HB2 3.41 HG12 2.79 HA 3.54 93 1367 HA 2.66 OG2.94 HE1 2.96 O 2.06 H 2.55 HB2 2.78 HZ 3.13 O 3.80 HB3 3.43 HG13 2.90HA 3.64 94 1371 HA 2.90 HG 3.39 HE2 3.12 O 2.49 H 2.74 HA 3.03 HZ 3.17 O3.87 HB2 3.27 HG13 2.75 HA 3.83 95 1372_A HA 2.62 OG 2.90 HE1 3.08 O2.07 H 2.46 HB2 2.72 HZ 3.15 O 3.71 HB2 3.30 HG13 2.87 HA 3.60 96 1372_BHA 2.61 OG 2.90 HE1 3.08 O 2.07 H 2.46 HB2 2.71 HZ 3.15 O 3.71 HB2 3.29HG13 2.86 HA 3.60 97 1373 HA 2.61 OG 2.89 HE1 3.10 O 2.12 H 2.49 HB22.71 HZ 3.12 O 3.73 HB2 3.29 HG13 2.89 HA 3.59 98 1492 HA 2.63 HG 3.14HE2 3.15 O 2.36 H 2.35 HB2 2.97 HZ 3.43 O 3.66 HB2 3.81 HG13 2.62 HA3.75 99 1399 HA 2.64 OG 2.86 HE1 3.10 O 2.11 H 2.50 HB2 2.71 HZ 3.25 O3.68 HB2 3.34 HG13 2.83 HA 3.60 100 1360 HA 2.60 OG 2.96 HE1 3.12 O 2.07H 2.49 HB2 2.62 HZ 3.13 O 3.74 HB3 3.38 HG12 2.87 HA 3.56 101 1368 HA2.65 OG 2.88 HE1 3.05 O 2.15 H 2.47 HB2 2.82 HZ 3.82 O 3.69 HB2 3.47HG12 2.82 HA 3.67 102 1406 HA 2.65 OG 2.75 HE1 3.16 O 2.09 H 2.63 HB22.58 HZ 3.22 O 3.70 HB2 3.19 HG12 2.80 HA 3.42 103 1411 HA 2.57 OG 2.92HE2 3.25 O 2.09 H 2.48 HB2 2.62 HZ 3.48 O 3.71 HB2 3.18 HG12 2.92 HA3.55 104 1433 HA 2.54 HG 3.36 HE1 3.53 O 2.32 H 2.28 HB2 2.71 HZ 3.26 O3.74 HB2 3.50 HG13 2.68 HA 3.71 105 1441 HA 2.62 OG 2.94 HE1 3.11 O 2.08H 2.50 HB2 2.75 HZ 3.51 O 3.79 HB3 3.41 HG12 2.87 HA 3.62 106 1435 HA2.60 OG 2.93 HE1 3.07 O 2.09 H 2.50 HB2 2.68 HZ 3.13 O 3.79 HB2 3.30HG13 2.81 HA 3.60 107 1450_A HA 2.59 OG 2.85 HE2 3.15 O 2.27 H 2.42 HB22.79 HZ 3.33 O 3.69 HB3 3.44 HG13 2.76 HA 3.70 108 1450_B HA 2.59 OG2.85 HE2 3.15 O 2.27 H 2.42 HB2 2.79 HZ 3.33 O 3.69 HB3 3.44 HG13 2.76HA 3.70 average distance 2.58 3.13 3.36 2.31 2.42 2.77 3.24 3.64 3.322.76 3.65 standard deviation 0.12 0.30 0.27 0.16 0.16 0.13 0.26 0.180.31 0.15 0.17 minimum value 2.32 2.36 2.60 2.04 2.03 2.36 2.56 2.962.70 1.96 3.37 maximum value 3.26 3.89 3.86 2.79 2.94 3.15 4.53 3.894.12 3.04 4.22 sample size 108 107 108 108 108 108 108 108 108 108 108Table A8-2 Pharmacophore protein distances Pharmacophore element C5 CA1N1 protein GLY_667 SER_628 TYR_669 TRP_655 VAL_668 SER_654 CYS_629GLY_656 TRP_655 CYS_629 ASP_627 1  14 HA3 2.61 HG 1.19 CZ 4.09 O 2.88 H2.83 H 3.85 HA 3.35 HA3 3.28 HA 3.62 HA 3.16 OD1 5.08 2 54_A HA3 2.66 OG2.24 HH 3.99 O 2.89 H 2.77 H 3.76 HA 3.15 H 3.49 HA 3.53 HA 3.03 OD15.27 3 54_B HA3 2.66 OG 2.24 HH 4.00 O 2.89 H 2.77 H 3.76 HA 3.15 H 3.49HA 3.53 HA 3.03 OD1 5.27 4 1129 HA3 2.59 HG 2.10 CZ 3.88 O 3.60 H 2.83 H3.77 HA 3.03 HA3 3.64 HA 3.91 HA 3.03 OD1 4.45 5 1034 HA3 2.60 OG 1.95CZ 4.01 O 3.77 H 3.36 H 3.86 HA 2.41 HA3 4.05 HA 3.96 HA 2.78 OD1 4.19 61024 HA3 2.80 HG 2.14 CZ 3.83 O 3.61 H 3.01 H 3.67 HA 3.01 HA3 3.76 HA3.65 HA 2.96 OD2 4.38 7 1042_1 HA2 2.94 OG 2.33 CE1 4.33 O 3.14 H 2.90 H3.72 HA 3.01 H 3.73 HA 3.50 HA 3.20 OD2 3.93 8 1042_2 HA2 3.14 OG 2.48CZ 3.92 O 3.38 H 3.01 H 4.11 HA 3.01 H 3.76 HA 3.77 HA 3.17 OD1 4.16 91042_3 HA2 3.12 OG 2.31 HE1 1.82 O 3.94 H 3.39 H 3.65 HA 2.57 H 4.52 HA3.87 HA 2.95 OD2 4.55 10 2018 HA3 2.96 HG 1.26 CZ 3.90 O 3.41 H 2.93 H3.56 HA 3.13 H 3.87 HA 3.65 HA 3.02 OD2 4.77 11 1059 HA3 2.77 OG 2.80 CZ3.71 O 3.47 H 2.91 H 3.60 HA 2.83 H 3.99 HA 3.58 HA 3.03 OD1 3.99 121088_A HA3 2.89 HG 2.65 HH 3.65 O 3.34 H 2.92 H 3.67 HA 3.26 HA3 3.73 HA3.63 HA 3.33 OD2 3.80 13 1088_B HA3 2.89 OG 2.75 CZ 3.73 O 3.34 H 2.92 H3.67 HA 3.26 HA3 3.73 HA 3.63 HA 3.33 OD2 3.80 14 1036_1 HA3 2.83 HG1.29 CZ 3.84 O 3.52 H 2.91 H 3.72 HA 2.94 H 3.74 HA 3.69 HA 2.99 OD24.61 15 1036_2_1 HA3 2.84 HG 2.49 CZ 3.79 O 3.32 H 2.71 H 3.80 HA 3.32HA3 4.19 HA 3.65 HA 3.21 OD1 4.47 16 1036_2_2 HA3 2.72 OG 2.48 HE1 3.77O 3.51 H 2.95 H 3.77 HA 2.90 H 3.39 HA 3.53 HA 2.91 OD2 4.76 17 1081 HA23.00 OG 2.66 CE1 3.70 O 3.53 H 3.33 H 3.76 HA 3.02 H 3.42 HA 3.56 HA3.18 OD2 4.39 18 1063 HA2 2.92 HG 1.90 CZ 3.88 O 3.60 H 3.07 H 3.86 HA3.24 H 3.38 HA 3.57 HA 3.35 OD1 4.24 19 1065 HA3 3.05 HG 2.33 CZ 3.80 O3.31 H 2.85 H 3.76 HA 3.10 H 3.61 HA 3.53 HA 3.27 OD2 4.05 20 1030_A HA32.83 HG 1.33 CZ 3.92 O 3.38 H 2.99 H 3.74 HA 2.96 N 3.92 HA 3.76 HA 3.14OD2 4.34 21 1030_B HA3 2.83 HG 1.33 CZ 3.92 O 3.38 H 2.99 H 3.74 HA 2.96N 3.92 HA 3.76 HA 3.14 OD2 4.34 22 1037 HA3 2.83 HB2 2.42 CE2 3.68 O3.18 H 2.77 H 3.83 HA 3.32 HA3 3.85 HA 3.64 HA 3.28 OD2 4.49 23 1118 HA32.81 HG 1.21 CZ 3.89 O 3.55 H 2.94 H 3.76 HA 3.08 H 3.85 HA 3.88 HA 3.22OD2 4.36 24 1090 HA2 3.12 OG 2.85 CZ 3.74 O 3.39 H 2.83 H 3.77 HA 2.93 H3.60 HA 3.55 HA 3.02 OD2 4.20 25 1007_1 HA3 3.06 HG 2.59 HH 3.62 O 3.06H 3.12 H 4.19 HA 3.14 HA3 3.37 HA 3.63 HA 3.32 OD2 3.20 26 1007_2 HA32.89 OG 2.76 CZ 3.68 O 3.17 H 3.22 H 4.00 HA 2.88 H 3.39 HA 3.43 HA 3.24OD2 3.37 27 1149 HA3 2.71 OG 2.00 HE1 3.74 O 2.99 O 3.22 H 3.78 HA 2.89HA3 4.06 HA 3.57 HA 2.99 OD2 3.98 28 1021_A HA3 3.04 OG 3.61 HH 3.36 O3.33 H 3.01 H 3.83 HA 3.16 H 3.29 HA 3.60 HA 3.26 OD2 3.84 29 1021_B HA33.04 OG 3.61 HH 3.35 O 3.34 H 3.01 H 3.83 HA 3.16 H 3.29 HA 3.60 HA 3.27OD2 3.83 30 1097_1 HA3 2.76 HG 1.68 CZ 3.84 O 3.54 H 2.65 H 3.67 HA 2.99N 4.02 HA 3.76 HA 3.04 OD2 4.46 31 1097_2 HA3 2.88 HG 1.75 CZ 3.88 O3.78 H 2.75 H 3.81 HA 2.99 H 3.89 HA 3.72 HA 3.06 OD2 4.47 32 1031_1 HA23.13 HB2 2.45 CZ 3.56 O 3.32 H 2.93 H 3.99 HA 3.17 H 3.34 HA 3.57 HA3.35 HD2 3.00 33 1031_2 HA2 3.12 HB2 2.47 CZ 3.59 O 3.29 H 2.95 H 3.97HA 3.21 H 3.30 HA 3.55 HA 3.39 HD2 3.04 34 1031_3 HA2 3.10 HB2 2.39 CZ3.63 O 3.36 H 2.98 H 4.01 HA 3.11 HA3 3.36 HA 3.67 HA 3.23 HD2 3.18 351031_4 HA2 3.11 HB2 2.42 CZ 3.62 O 3.31 H 2.92 H 4.02 HA 3.16 HA3 3.27HA 3.62 HA 3.21 OD2 3.69 36 1153_A HA2 2.70 HG 1.40 CE1 3.91 O 3.48 H2.84 H 3.71 HA 3.02 H 3.80 HA 3.79 HA 3.02 OD2 4.25 37 1153_B HA2 2.70HG 3.38 CE1 3.91 O 3.48 H 2.84 H 3.73 HA 3.02 H 3.80 HA 3.79 HA 3.02 OD24.25 38 1025_1 HA3 3.07 OG 3.31 CE1 4.03 O 3.45 H 3.11 H 3.83 HA 2.96HA3 3.37 HA 3.66 HA 3.05 OD1 3.74 39 1025_2 HA2 3.21 HG 2.29 CE1 3.73 O3.28 H 3.10 H 3.97 HA 3.17 H 4.13 HA 3.69 HA 3.24 OD1 3.81 40 1025_3 HA22.99 OG 2.86 HH 3.03 O 3.18 H 3.53 H 3.83 HA 3.05 HA3 3.06 HA 3.54 HA3.25 OD2 3.71 41 1025_4 HA3 3.19 HG 2.68 HH 3.68 O 3.19 H 3.20 H 4.07 HA3.11 HA3 3.52 HA 3.63 HA 3.17 OD2 3.79 42 1025_5 HA3 3.01 HG 2.24 HH3.46 O 3.27 H 3.24 H 3.90 HA 2.63 H 3.70 HA 3.55 HA 2.84 OD2 3.97 431025_6 HA3 2.96 OG 2.87 CZ 3.95 O 3.13 O 3.34 H 3.94 HA 3.13 H 3.72 HA3.34 HA 3.16 OD1 3.53 44 1089_A HA3 2.97 OG 2.85 CZ 3.82 O 3.43 H 2.90 H3.57 HA 3.21 H 3.74 HA 3.54 HA 3.23 OD2 4.10 45 1089_B HA3 2.97 OG 2.85CZ 3.82 O 3.43 H 2.90 H 3.57 HA 3.21 H 3.74 HA 3.54 HA 3.23 OD2 4.10 461012_1 HA3 3.13 OG 2.72 CZ 3.68 O 3.22 H 2.96 H 3.78 HA 2.99 H 3.31 HA3.53 HA 3.26 OD2 3.43 47 1012_2 HA3 3.10 HG 2.00 CZ 3.67 O 3.22 H 2.80 H3.89 HA 3.09 H 3.33 HA 3.54 HA 3.29 OD2 3.40 48 1078_1 HA3 3.00 HG 2.96CZ 3.64 O 3.45 H 2.92 H 3.73 HA 3.15 H 3.21 HA 3.53 HA 3.39 OD2 3.32 491078_10 HA3 3.10 HG 2.45 CZ 3.65 O 3.50 H 2.99 H 3.60 HA 3.08 H 3.37 HA3.55 HA 3.30 HD2 2.86 50 1078_11 HA3 3.01 HG 2.47 CZ 3.63 O 3.45 H 2.92H 3.73 HA 3.14 H 3.21 HA 3.53 HA 3.38 HD2 2.77 51 1078_12 HA3 2.95 HG2.54 CZ 3.64 O 3.46 H 2.92 H 3.77 HA 3.14 H 3.22 HA 3.55 HA 3.40 HD22.70 52 1078_13 HA3 3.00 HG 2.51 HH 3.50 O 3.46 H 2.93 H 3.73 HA 3.14 H3.23 HA 3.54 HA 3.39 HD2 2.71 53 1078_14 HA3 2.97 HG 2.48 CZ 3.61 O 3.48H 2.95 H 3.75 HA 3.13 H 3.26 HA 3.57 HA 3.39 HD2 2.70 54 1078_15 HA32.98 HG 2.47 HH 3.53 O 3.46 H 2.93 H 3.75 HA 3.13 H 3.22 HA 3.55 HA 3.38HD2 2.73 55 1078_16 HA3 2.97 HG 2.49 HH 3.54 O 3.46 H 2.91 H 3.76 HA3.17 H 3.21 HA 3.57 HA 3.41 HD2 2.73 56 1078_2 HA3 2.96 HG 2.47 HH 3.48O 3.48 H 2.95 H 3.77 HA 3.12 H 3.24 HA 3.58 HA 3.38 HD2 2.70 57 1078_3HA3 3.07 HG 2.41 CZ 3.62 O 3.50 H 3.00 H 3.70 HA 3.02 H 3.32 HA 3.56 HA3.26 HD2 2.79 58 1078_4 HA3 2.95 HG 2.50 CZ 3.63 O 3.45 H 2.90 H 3.77 HA3.14 H 3.20 HA 3.55 HA 3.40 HD2 2.70 59 1078_5 HA3 3.00 HG 2.49 HH 3.53O 3.45 H 2.93 H 3.74 HA 3.14 H 3.20 HA 3.54 HA 3.38 HD2 2.72 60 1078_6HA3 2.98 HG 2.50 CZ 3.64 O 3.48 H 2.94 H 3.75 HA 3.17 H 3.23 HA 3.57 HA3.41 HD2 2.73 61 1078_7 HA3 3.00 HG 2.52 HH 3.50 O 3.44 H 2.92 H 3.72 HA3.15 H 3.20 HA 3.53 HA 3.38 HD2 2.73 62 1078_8 HA3 2.99 HG 2.50 CZ 3.64O 3.46 H 2.91 H 3.73 HA 3.15 H 3.21 HA 3.53 HA 3.37 HD2 2.77 63 1078_9HA3 2.96 HG 2.52 HH 3.51 O 3.43 H 2.89 H 3.75 HA 3.14 H 3.18 HA 3.55 HA3.42 HD2 2.67 64 1145_A HA3 2.49 HG 1.41 CZ 3.81 O 3.46 H 2.81 H 3.66 HA3.04 H 3.58 HA 3.75 HA 3.13 OD2 4.31 65 1145_B HA3 2.49 HG 1.41 CZ 3.81O 3.46 H 2.81 H 3.66 HA 3.04 H 3.58 HA 3.75 HA 3.13 OD2 4.31 66 1050 HA32.73 HG 1.60 CZ 3.82 O 3.17 H 3.10 H 3.83 HA 3.07 HA3 3.83 HA 3.62 HA3.09 OD2 4.56 67 1253 HA3 3.24 HB2 2.53 CZ 3.71 O 3.19 H 2.92 H 3.50 HA2.98 H 3.31 HA 3.43 HA 3.15 OD2 3.62 68 1257 HA3 3.08 HG 2.17 CZ 3.70 O3.31 H 2.87 H 3.58 HA 3.08 H 3.40 HA 3.49 HA 3.30 OD2 3.82 69 999_1 HA22.82 OG 2.54 CZ 3.93 O 3.27 H 2.80 H 3.92 HA 2.20 HA3 3.86 HA 3.71 HA2.75 OD2 4.47 70 999_2_A HA3 2.79 OG 2.07 CZ 3.86 O 3.19 H 2.71 H 3.79HA 3.05 HA3 3.65 HA 3.83 HA 3.08 OD1 4.44 71 999_2_B HA3 2.79 OG 2.07 CZ3.86 O 3.19 H 2.71 H 3.79 HA 3.05 HA3 3.65 HA 3.83 HA 3.08 OD1 4.44 721297_1 HA3 3.02 OG 2.89 CZ 3.75 O 3.19 H 2.89 H 3.68 HA 2.88 HA3 3.43 HA3.36 HA 3.09 OD2 3.33 73 1297_2 HA3 2.99 HB2 3.24 CZ 3.67 O 3.21 H 2.88H 3.70 HA 2.91 HA3 3.47 HA 3.36 HA 3.12 OD2 3.31 74 1297_3 HA3 3.01 OG2.86 CZ 3.71 O 3.22 H 2.90 H 3.66 HA 2.84 HA3 3.44 HA 3.42 HA 3.11 OD23.29 75 1297_4 HA3 2.98 HB2 3.25 CZ 3.65 O 3.20 H 2.87 H 3.70 HA 2.89HA3 3.45 HA 3.36 HA 3.13 OD2 3.30 76 1297_5 HA3 2.99 HG 2.38 HH 3.57 O3.24 H 2.95 H 3.66 HA 2.80 HA3 3.52 HA 3.40 HA 3.09 OD2 3.25 77 1297_6HA3 3.02 OG 2.87 CZ 3.71 O 3.26 H 2.97 H 3.64 HA 2.76 HA3 3.53 HA 3.44HA 3.08 OD2 3.23 78 1304 HA3 3.20 HB2 2.57 CZ 3.71 O 3.19 H 2.95 H 3.49HA 3.05 H 3.39 HA 3.42 HA 3.20 OD2 3.45 79 1306_1 HA3 2.72 OG 2.26 CZ3.52 O 3.65 H 3.07 H 3.33 HA 3.62 N 3.71 HA 3.40 HA 3.64 OD1 4.28 801306_2 HA3 2.74 HG 1.92 CZ 3.60 O 3.43 H 3.03 H 3.49 HA 3.11 HA3 3.60 HA3.43 HA 3.32 OD2 4.34 81 1307 HA3 3.20 HB2 2.60 CZ 3.70 O 3.32 H 2.87 H3.42 HA 3.37 H 3.24 HA 3.39 HA 3.36 OD1 4.13 82 1328_1 HA3 3.12 OG 2.56CZ 3.77 O 3.22 H 2.85 H 3.76 HA 2.97 H 3.01 HA 3.38 HA 3.27 OD2 3.14 831328_2 HA3 3.15 HB2 2.59 CZ 3.73 O 3.22 H 2.87 H 3.75 HA 2.95 H 3.04 HA3.39 HA 3.21 OD2 3.17 84 1328_3 HA3 3.06 HB2 2.51 CZ 3.71 O 3.32 H 2.91H 3.83 HA 3.03 H 3.10 HA 3.49 HA 3.27 OD2 3.24 85 1328_4 HA3 3.12 HB22.59 CZ 3.63 O 3.36 H 2.93 H 3.74 HA 2.98 H 3.16 HA 3.46 HA 3.27 OD23.16 86 1334 HA3 3.01 HB2 2.69 CZ 3.83 O 3.46 H 2.88 H 3.85 HA 2.95 HA33.36 HA 3.74 HA 3.08 OD2 4.09 87 1335 HA3 2.77 HG 1.38 CZ 3.89 O 3.50 H2.95 H 3.72 HA 3.03 H 3.76 HA 3.75 HA 3.10 OD2 4.50 88 1338 HA3 3.27 HB22.50 CZ 3.83 O 3.22 H 2.87 H 3.57 HA 3.03 H 3.26 HA 3.36 HA 3.26 OD23.50 89 1345_1 HA2 2.74 HG 2.73 CZ 3.85 O 3.27 H 2.48 H 3.39 HA 3.38 HA33.10 HA 3.39 HA 3.39 OD2 4.56 90 1345_2 HA2 2.50 OG 2.17 CE1 3.88 H 3.66H 2.79 H 3.65 HA 2.85 H 3.85 HA 3.70 HA 2.93 OD2 4.39 91 1351 HA2 3.17HB2 2.44 CZ 3.72 O 3.30 H 2.98 H 3.78 HA 2.99 H 3.28 HA 3.51 HA 3.24 OD23.29 92 1353 HA3 3.18 HB2 2.52 CZ 3.74 O 3.25 H 2.96 H 3.43 HA 3.08 H3.31 HA 3.32 HA 3.21 OD2 3.49 93 1367 HA3 3.18 HB2 2.52 CZ 3.73 O 3.23 H2.92 H 3.41 HA 3.02 H 3.23 HA 3.45 HA 3.18 OD2 3.54 94 1371 HA2 2.97 OG2.59 CZ 3.52 O 3.49 H 3.12 H 3.59 HA 3.18 HA3 3.61 HA 3.63 HA 3.42 OD13.75 95 1372_A HA3 3.20 HB2 2.60 CZ 3.74 O 3.19 H 2.89 H 3.50 HA 2.98 H3.34 HA 3.41 HA 3.13 OD2 3.46 96 1372_B HA3 3.20 HB2 2.60 CZ 3.73 O 3.19H 2.89 H 3.50 HA 2.98 H 3.34 HA 3.41 HA 3.13 OD2 3.46 97 1373 HA3 3.23HB2 2.56 CZ 3.70 O 3.21 H 2.91 H 3.48 HA 2.96 H 3.24 HA 3.43 HA 3.14 OD23.47 98 1492 HA2 2.81 OG 2.44 CZ 3.90 O 3.53 H 3.10 H 3.89 HA 3.05 H3.70 HA 3.69 HA 3.13 OD1 3.90 99 1399 HA3 3.23 HB2 2.54 CZ 3.71 O 3.17 H2.91 H 3.45 HA 3.01 H 3.26 HA 3.42 HA 3.16 OD2 3.55 100 1360 HA3 3.23HB2 2.53 CZ 3.75 O 3.24 H 2.92 H 3.48 HA 3.06 H 3.47 HA 3.37 HA 3.23 OD23.51 101 1368 HA3 3.15 HB2 2.53 CZ 3.73 O 3.21 H 2.91 H 3.51 HA 3.19 H3.40 HA 3.47 HA 3.28 OD2 3.59 102 1406 HA3 3.18 HB2 2.59 CZ 3.68 O 3.06H 2.89 H 3.47 HA 3.07 H 3.44 HA 3.22 HA 3.23 OD2 3.49 103 1411 HA3 3.33HB2 2.57 CZ 3.73 O 3.25 H 3.01 H 3.43 HA 3.11 H 3.35 HA 3.31 HA 3.28 OD23.35 104 1433 HA3 3.08 HB2 2.59 CZ 3.67 O 3.44 H 2.80 H 3.61 HA 3.09 H3.36 HA 3.58 HA 3.12 OD2 4.15 105 1441 HA3 3.23 HB2 2.53 CZ 3.68 O 3.24H 2.93 H 3.46 HA 3.03 H 3.30 HA 3.46 HA 3.21 OD2 3.53 106 1435 HA3 3.20HB2 2.60 CZ 3.69 O 3.21 H 2.93 H 3.49 HA 2.98 H 3.36 HA 3.41 HA 3.18 OD23.56 107 1450_A HA3 3.10 HB2 2.53 CZ 3.69 O 3.32 H 2.89 H 3.58 HA 3.18 H3.34 HA 3.55 HA 3.22 OD2 3.94 108 1450_B HA3 3.10 HB2 2.53 CZ 3.69 O3.32 H 2.89 H 3.58 HA 3.18 H 3.34 HA 3.55 HA 3.22 OD2 3.94 averagedistance 2.97 2.39 3.71 3.34 2.94 3.71 3.05 3.49 3.56 3.20 3.75 standarddeviation 0.19 0.48 0.25 0.18 0.15 0.16 0.18 0.28 0.14 0.15 0.63 minimumvalue 2.49 1.19 1.82 2.88 2.48 3.33 2.20 3.01 3.22 2.75 2.67 maximumvalue 3.33 3.61 4.33 3.94 3.53 4.19 3.62 4.52 3.96 3.64 5.27 sample size108 108 108 108 108 108 108 108 108 108 108 Table A8-3 Pharmacophoreprotein distances Pharmacophore element N1 C7 O4 protein GLY_667 GLY_656SER_628 CYS_660 CYS_629 GLY_661 ASP_627 SER_657 GLY_656 SER_628 CYS_6601  14 HA2 3.80 HA3 2.39 O 3.27 HA 3.82 HA 3.17 H 4.04 HB3 5.20 O 2.68HA3 3.17 O 3.50 HA 5.32 2 54_A HA2 3.78 HA3 2.55 O 3.09 HA 3.39 HA 3.09H 4.22 HB3 5.19 H 2.75 HA3 3.30 O 3.38 HB2 4.19 3 54_B HA2 3.78 HA3 2.55O 3.09 HA 3.39 HA 3.09 H 4.22 HB3 5.19 H 2.75 HA3 3.30 O 3.38 HB2 4.19 41129 HA2 3.57 HA3 3.00 O 2.95 HG 1.07 HA 3.35 H 4.30 OD2 4.25 O 3.25 HA33.56 O 3.67 HG 3.37 5 1034 HA2 3.67 HA3 3.36 O 2.57 HB3 1.55 HA 3.46 H4.11 OD2 4.11 O 3.50 HA3 3.90 O 3.43 HB3 3.80 6 1024 HA2 3.79 HA3 2.97 O2.94 HA 2.63 HA 3.32 H 4.34 OD2 3.87 O 3.08 HA3 3.52 O 3.64 HB2 5.18 71042_1 HA2 3.84 HA3 3.11 O 3.06 HA 2.49 HA 3.56 H 4.00 OD2 3.49 O 3.06HA3 3.77 O 3.59 SG 4.30 8 1042_2 HA2 4.12 HA3 3.26 O 4.59 HA 2.46 HA3.89 H 3.85 OD2 4.45 O 2.74 HA3 3.95 O 5.00 SG 4.34 9 1042_3 HA2 4.11HA3 3.89 OG 3.18 HA 3.22 SG 2.61 H 3.35 OD2 4.07 O 2.89 HA3 4.36 OG 4.62SG 4.32 10 2018 HA2 3.93 HA3 3.36 O 3.05 HB3 2.22 HA 3.24 H 4.46 OD24.21 O 2.85 HA3 3.91 O 3.56 HB3 4.02 11 1059 HA2 3.82 HA3 3.55 O 3.27 HA2.40 HA 3.49 H 4.22 OD2 3.60 O 3.26 HA3 4.07 O 3.72 SG 3.37 12 1088_AHA2 3.96 HA3 2.90 O 3.26 HB3 2.40 HA 3.60 H 4.02 OD2 3.39 O 3.46 HA33.40 O 3.78 HB3 3.93 13 1088_B HA2 3.96 HA3 2.90 O 3.26 HB3 2.40 HA 3.60H 4.02 OD2 3.39 O 3.46 HA3 3.40 O 3.78 HB3 3.93 14 1036_1 HA2 3.76 HA33.15 O 3.05 HA 2.64 HA 3.25 H 4.40 OD2 4.08 O 3.18 HA3 3.69 O 3.48 SG3.82 15 1036_2_1 HA2 3.69 HA3 3.48 O 2.98 HA 2.71 HA 3.41 H 4.19 OD24.41 O 3.09 HA3 4.03 O 3.68 SG 5.28 16 1036_2_2 HA2 3.74 HA3 3.30 O 2.73HA 2.43 HA 3.23 H 4.34 OD2 4.20 O 3.06 HA3 3.82 O 3.55 H 4.53 17 1081HA2 4.01 HA3 3.25 O 2.87 HA 2.48 HA 3.59 H 3.74 OD2 4.05 O 3.21 HA3 3.73O 3.64 HB2 4.46 18 1063 HA2 3.83 HA3 2.94 O 3.28 HA 2.51 HA 3.65 H 4.01OD2 4.01 O 3.03 HA3 3.42 O 3.70 SG 4.21 19 1065 HA2 4.07 HA3 3.00 O 2.95HA 2.37 HA 3.59 H 3.79 OD2 3.53 O 3.21 HA3 3.57 O 3.55 HB2 4.72 201030_A HA2 3.81 HA3 3.29 O 3.35 HA 2.46 HA 3.45 H 4.14 OD2 3.82 O 2.96HA3 3.89 O 3.68 SG 3.54 21 1030_B HA2 3.81 HA3 3.29 O 3.35 HA 2.46 HA3.45 H 4.14 OD2 3.82 O 2.96 HA3 3.89 O 3.68 SG 3.54 22 1037 HA2 3.72 HA33.08 O 2.71 HA 2.55 HA 3.54 H 4.19 OD2 4.00 O 3.16 HA3 3.65 O 3.61 HB24.31 23 1118 HA2 3.81 HA3 3.28 O 3.18 HA 2.33 HA 3.46 H 4.00 OD2 3.83 O3.28 HA3 3.80 O 3.53 HB2 4.31 24 1090 HA2 3.94 HA3 2.83 O 3.36 HA 2.28HA 3.50 H 3.98 OD2 3.81 O 3.17 HA3 3.31 O 3.87 HB2 4.16 25 1007_1 HA24.04 HA3 2.51 O 2.88 HA 2.14 HA 3.64 H 3.49 OD2 2.89 O 2.65 HA3 3.31 O4.02 HB2 3.76 26 1007_2 HA2 3.98 HA3 2.63 O 2.70 HA 2.28 HA 3.64 H 3.40OD2 3.01 O 2.38 HA3 3.38 O 3.55 HB2 4.10 27 1149 HA2 3.66 HA3 3.20 O3.03 HA 2.70 HA 3.20 H 3.83 OD2 3.39 O 2.94 HA3 3.88 O 3.30 SG 3.83 281021_A HA2 4.00 HA3 2.53 O 2.86 HA 2.61 HA 3.43 H 3.83 OD2 3.28 O 2.74HA3 3.23 O 3.50 HB2 4.61 29 1021_B HA2 3.99 HA3 2.54 O 2.86 HA 2.61 HA3.44 H 3.82 OD2 3.27 O 2.75 HA3 3.23 O 3.50 HB2 4.61 30 1097_1 HA2 3.60HA3 3.31 O 2.90 HA 2.36 HA 3.37 H 4.09 OD2 3.95 O 3.21 HA3 3.84 O 3.56HB2 4.35 31 1097_2 HA2 3.70 HA3 3.16 O 2.89 HA 2.28 HA 3.33 H 4.07 OD23.96 O 3.18 HA3 3.70 O 3.48 HB2 4.24 32 1031_1 HA2 4.16 HA3 2.38 O 3.36HA 2.62 HA 3.61 H 3.17 HD2 3.11 H 2.71 HA3 3.10 O 3.70 SG 3.80 33 1031_2HA2 4.15 HA3 2.35 O 3.39 HA 2.60 HA 3.68 H 3.05 HD2 3.14 H 2.71 HA3 3.06O 3.75 SG 3.81 34 1031_3 HA2 4.17 HA3 2.39 O 3.37 HA 3.08 HA 3.53 H 3.10HD2 3.23 H 2.63 HA3 3.14 O 3.71 HA 4.96 35 1031_4 HA2 4.18 HA3 2.27 O3.42 HA 3.12 HA 3.47 H 3.03 OD2 3.46 H 2.64 HA3 3.02 O 3.75 HA 4.96 361153_A HA2 3.57 HA3 3.17 O 3.35 SG 2.74 HA 3.34 H 4.47 OD2 3.81 O 2.56HA3 3.77 O 3.78 SG 4.17 37 1153_B HA2 3.57 HA3 3.17 O 3.35 SG 2.74 HA3.34 H 4.47 OD2 3.81 O 2.56 HA3 3.77 O 3.78 SG 4.17 38 1025_1 HA2 4.26HA3 2.47 O 2.67 HA 2.27 HA 3.42 H 3.52 OD2 3.57 O 2.77 HA3 3.14 O 3.62HB2 3.76 39 1025_2 HA2 4.17 HA3 3.43 O 2.66 HA 2.71 HA 3.48 H 3.62 OD23.59 O 2.61 HA3 3.99 O 3.70 HB2 3.70 40 1025_3 HA2 4.09 HA3 2.17 O 2.63HA 2.34 HA 3.60 H 3.23 OD2 3.36 O 3.02 HA3 2.80 O 3.74 HB2 4.55 411025_4 HA2 4.16 HA3 2.69 O 2.70 HA 2.30 HA 3.51 H 3.27 OD2 3.26 O 2.84HA3 3.34 O 3.76 HB2 4.06 42 1025_5 HA2 4.12 HA3 3.07 O 2.73 HA 2.74 HA3.35 H 3.76 OD2 3.53 O 2.89 HA3 3.67 O 3.96 HA 5.06 43 1025_6 HA2 4.28HA3 3.11 O 2.58 HA 2.18 HA 3.37 H 3.69 OD2 2.92 H 2.52 HA3 3.77 O 3.37HB2 3.78 44 1089_A HA2 4.01 HA3 3.03 O 3.30 HB3 2.29 HA 3.51 H 4.12 OD23.66 O 3.12 HA3 3.54 O 3.76 HB3 3.95 45 1089_B HA2 4.01 HA3 3.03 O 3.30HB3 2.29 HA 3.51 H 4.12 OD2 3.66 O 3.12 HA3 3.54 O 3.76 HB3 3.95 461912_1 HA2 4.13 HA3 2.71 O 3.01 HA 2.33 HA 3.54 H 3.54 OD2 3.03 O 2.58HA3 3.36 O 3.51 SG 3.69 47 1012_2 HA2 4.01 HA3 2.56 O 2.99 HA 2.31 HA3.57 H 3.56 OD2 3.08 O 2.67 HA3 3.25 O 3.54 SG 3.65 48 1078_1 HA2 4.00HA3 2.47 O 3.07 HA 2.30 HA 3.77 H 3.50 OD2 2.95 H 2.77 HA3 3.16 O 3.70SG 3.59 49 1078_0 HA2 4.04 HA3 2.62 O 3.03 HA 2.30 HA 3.64 H 3.55 HD22.75 H 2.97 HA3 3.22 O 3.61 SG 3.59 50 1078_11 HA2 3.97 HA3 2.47 O 3.07HA 2.29 HA 3.76 H 3.52 HD2 2.73 H 2.74 HA3 3.16 O 3.70 SG 3.65 511078_12 HA2 3.97 HA3 2.49 O 3.07 HA 2.24 HA 3.80 H 3.47 HD2 2.67 H 2.78HA3 3.20 O 3.72 SG 3.59 52 1078_13 HA2 3.99 HA3 2.47 O 3.06 HA 2.28 HA3.77 H 3.50 HD2 2.66 H 2.77 HA3 3.15 O 3.69 SG 3.61 53 1078_14 HA2 3.96HA3 2.50 O 3.08 HA 2.22 HA 3.79 H 3.45 HD2 2.67 H 2.78 HA3 3.20 O 3.73SG 3.54 54 1078_15 HA2 3.98 HA3 2.45 O 3.05 HA 2.26 HA 3.77 H 3.47 HD22.70 H 2.75 HA3 3.15 O 3.70 SG 3.46 55 1078_16 HA2 3.97 HA3 2.48 O 3.09HA 2.25 HA 3.80 H 3.49 HD2 2.70 H 2.76 HA3 3.19 O 3.73 SG 3.60 56 1078_2HA2 3.97 HA3 2.47 O 3.05 HA 2.30 HA 3.77 H 3.50 HD2 2.63 H 2.78 HA3 3.18O 3.70 SG 3.58 57 1078_3 HA2 4.08 HA3 2.57 O 2.99 HA 2.30 HA 3.64 H 3.54HD2 2.73 H 2.88 HA3 3.21 O 3.63 SG 3.53 58 1078_4 HA2 3.96 HA3 2.43 O3.06 HA 2.25 HA 3.79 H 3.47 HD2 2.66 H 2.72 HA3 3.15 O 3.70 SG 3.63 591078_5 HA2 3.98 HA3 2.46 O 3.07 HA 2.28 HA 3.78 H 3.48 HD2 2.68 H 2.70HA3 3.17 O 3.71 SG 3.61 60 1078_6 HA2 3.99 HA3 2.49 O 3.08 HA 2.26 HA3.80 H 3.49 HD2 2.69 H 2.74 HA3 3.20 O 3.72 SG 3.64 61 1078_7 HA2 3.98HA3 2.47 O 3.06 HA 2.29 HA 3.77 H 3.50 HD2 2.66 H 2.76 HA3 3.15 O 3.70SG 3.62 62 1078_8 HA2 3.97 HA3 2.44 O 3.07 HA 2.27 HA 3.74 H 3.52 HD22.71 H 2.76 HA3 3.13 O 3.69 SG 3.64 63 1078_9 HA2 3.98 HA3 2.45 O 3.05HA 2.22 HA 3.83 H 3.42 HD2 2.64 H 2.71 HA3 3.17 O 3.71 SG 3.57 64 1145_AHA2 3.55 HA3 3.14 O 3.15 HA 2.66 HA 3.37 H 4.43 OD2 3.80 O 2.98 HA3 3.70O 3.57 HB2 4.52 65 1145_B HA2 3.55 HA3 3.14 O 3.15 HA 2.66 HA 3.37 H4.43 OD2 3.80 O 2.98 HA3 3.70 O 3.57 HB2 4.52 66 1050 HA2 3.67 HA3 3.07O 3.15 HA 2.58 HA 3.29 H 4.25 OD2 4.13 O 2.89 HA3 3.61 O 3.54 SG 3.61 671253 HA2 4.18 HA3 2.67 O 2.85 HA 2.45 HA 3.45 H 3.82 OD2 3.11 O 2.79 HA33.25 O 3.42 SG 3.72 68 1257 HA2 4.07 HA3 2.72 O 2.73 HA 2.25 HA 3.59 H3.98 OD2 3.31 O 3.00 HA3 3.30 O 3.44 HB2 4.14 69 999_1 HA2 3.85 HA3 3.03O 2.72 HB2 2.47 HB3 2.93 H 4.30 OD2 3.98 O 2.72 HA3 3.61 O 3.28 HB2 4.1270 999_2_A HA2 3.67 HA3 2.87 O 2.91 HB2 2.39 HA 3.40 H 3.82 OD2 4.09 O3.09 HA3 3.49 O 3.54 HB2 4.00 71 999_2_B HA2 3.67 HA3 2.87 O 2.91 HB22.39 HA 3.40 H 3.82 OD2 4.09 O 3.09 HA3 3.49 O 3.54 HB2 4.00 72 1297_1HA2 4.11 HA3 2.49 O 2.88 HA 2.23 HA 3.45 H 3.36 OD2 2.99 O 2.75 HA3 3.13O 3.54 HB2 4.37 73 1297_2 HA2 4.10 HA3 2.55 O 2.85 HA 2.25 HA 3.45 H3.36 OD2 2.96 O 2.76 HA3 3.17 O 3.50 HB2 4.41 74 1297_3 HA2 4.08 HA32.52 O 2.84 HA 2.18 HA 3.47 H 3.29 OD2 2.93 O 2.83 HA3 3.13 O 3.51 HB24.28 75 1297_4 HA2 4.09 HA3 2.53 O 2.84 HA 2.26 HA 3.47 H 3.35 OD2 2.94O 2.77 HA3 3.17 O 3.50 HB2 4.29 76 1297_5 HA2 4.11 HA3 2.61 O 2.81 HA2.17 HA 3.47 H 3.27 OD2 2.92 O 2.86 HA3 3.22 O 3.51 HB2 4.17 77 1297_6HA2 4.10 HA3 2.61 O 2.80 HA 2.17 HA 3.48 H 3.25 OD2 2.88 O 2.88 HA3 3.21O 3.50 HB2 4.12 78 1304 HA2 4.17 HA3 2.63 O 2.95 HA 2.44 HA 3.48 H 3.74OD2 3.01 O 2.78 HA3 3.21 O 3.48 SG 3.73 79 1306_1 HA2 3.21 HA3 3.11 O3.37 HA 2.51 HA 3.73 H 4.27 OD2 3.70 O 3.12 HA3 3.40 O 3.72 HB2 3.84 801306_2 HA2 3.35 HA3 2.71 O 3.38 HA 2.76 HA 3.66 H 4.32 OD2 3.75 O 2.86HA3 3.12 O 3.80 SG 4.28 81 1307 HA2 4.13 HA3 2.69 O 3.42 HA 2.56 HA 3.46H 4.14 OD2 3.57 O 3.04 HA3 3.30 O 3.67 SG 4.18 82 1328_1 HA2 4.16 HA32.33 O 3.00 HB3 2.07 HA 3.70 H 3.41 OD2 3.04 O 2.52 HA3 3.05 O 3.63 HB33.28 83 1328_2 HA2 4.18 HA3 2.41 O 2.92 HA 2.10 HA 3.57 H 3.47 OD2 2.99O 2.57 HA3 3.12 O 3.51 SG 3.61 84 1328_3 HA2 4.14 HA3 2.41 O 2.96 HA2.08 HA 3.65 H 3.50 OD2 3.08 O 2.51 HA3 3.15 O 3.57 SG 3.63 85 1328_4HA2 4.11 HA3 2.44 O 2.87 HA 2.08 HA 3.62 H 3.46 OD2 2.96 O 2.63 HA3 3.12O 3.48 SG 3.62 86 1334 HA2 4.04 HA3 2.47 O 3.33 SG 2.65 HA 3.44 H 4.18OD2 3.53 O 2.93 HA3 3.12 O 3.72 SG 3.64 87 1335 HA2 3.79 HA3 3.32 O 3.27HA 2.68 HA 3.37 H 4.39 OD2 3.96 O 2.92 HA3 3.85 O 3.60 SG 3.75 88 1338HA2 4.26 HA3 2.79 O 2.85 HA 2.32 HA 3.54 H 3.69 OD2 3.02 O 2.74 HA3 3.36O 3.50 HB2 4.64 89 1345_1 HA2 3.45 HA3 2.29 O 3.43 HA 2.91 HA 3.46 H4.47 OD2 3.95 O 3.08 HA3 2.71 O 3.64 SG 3.92 90 1345_2 HA2 3.63 HA3 3.12O 3.00 HA 2.72 HA 3.01 H 4.49 OD2 3.68 O 3.48 HA3 3.60 O 3.14 SG 3.73 911351 HA2 4.12 HA3 2.66 O 2.90 HA 2.21 HA 3.50 H 3.54 OD2 2.87 O 2.67 HA33.25 O 3.48 SG 3.62 92 1353 HA2 4.18 HA3 2.69 O 3.02 HA 2.46 HA 3.45 H3.76 OD2 3.02 O 2.72 HA3 3.27 O 3.50 SG 3.86 93 1367 HA2 4.19 HA3 3.00 O2.96 HA 2.47 HA 3.46 H 3.80 OD2 3.09 O 2.58 HA3 3.60 O 3.49 SG 3.77 941371 HA2 3.95 HA3 2.66 O 3.05 HA 2.38 HA 3.70 H 3.84 OD2 3.21 O 3.05 HA33.23 O 3.59 SG 3.47 95 1372_A HA2 4.19 HA3 2.70 O 2.96 HA 2.47 HA 3.41 H3.89 OD2 3.00 O 2.74 HA3 3.28 O 3.48 SG 3.72 96 1372_B HA2 4.18 HA3 2.70O 2.95 HA 2.47 HA 3.41 H 3.89 OD2 3.00 O 2.75 HA3 3.27 O 3.48 SG 3.72 971373 HA2 4.18 HA3 2.78 O 2.94 HA 2.42 HA 3.44 H 3.83 OD2 3.01 O 2.76 HA33.33 O 3.47 SG 3.74 98 1492 HA2 3.81 HA3 3.40 O 3.38 HA 2.22 HA 3.57 H4.06 OD2 3.99 O 3.30 HA3 3.91 O 3.86 HB2 3.95 99 1399 HA2 4.16 HA3 2.68O 2.90 HA 2.41 HA 3.42 H 3.88 OD2 3.06 O 2.76 HA3 3.25 O 3.44 SG 3.79100 1360 HA2 4.20 HA3 2.64 O 3.00 HA 2.47 HA 3.48 H 3.77 OD2 3.05 O 2.77HA3 3.24 O 3.52 SG 3.78 101 1368 HA2 4.14 HA3 2.63 O 2.94 HA 2.48 HA3.48 H 3.91 OD2 3.12 O 2.79 HA3 3.23 O 3.51 SG 3.83 102 1406 HA2 4.12HA3 2.62 O 3.06 HA 2.37 HA 3.51 H 3.84 OD2 3.12 O 2.71 HA3 3.14 O 3.60SG 3.83 103 1411 HA2 4.23 HA3 2.87 O 3.03 HG 1.74 HA 3.53 H 3.80 OD23.00 O 2.64 HA3 3.39 O 3.58 HG 3.02 104 1433 HA2 4.03 HA3 2.60 O 3.35 HA2.82 HA 3.34 H 4.31 OD2 3.58 O 2.94 HA3 3.17 O 3.65 SG 3.89 105 1441 HA24.16 HA3 2.78 O 2.84 HA 2.47 HA 3.48 H 3.81 OD2 3.04 O 2.82 HA3 3.35 O3.46 SG 3.79 106 1435 HA2 4.13 HA3 2.80 O 2.95 HA 2.40 HA 3.48 H 3.82OD2 3.07 O 2.77 HA3 3.37 O 3.49 SG 3.67 107 1450_A HA2 4.06 HA3 2.70 O3.10 HA 2.73 HA 3.39 H 4.06 OD2 3.41 O 2.88 HA3 3.30 O 3.54 SG 4.12 1081450_B HA2 4.06 HA3 2.70 O 3.10 HA 2.73 HA 3.39 H 4.06 OD2 3.41 O 2.88HA3 3.30 O 3.54 SG 4.12 average distance 3.96 2.79 3.05 2.44 3.49 3.823.41 2.87 3.40 3.62 3.98 standard deviation 0.21 0.34 0.26 0.33 0.200.37 0.57 0.23 0.30 0.22 0.43 minimum value 3.21 2.17 2.57 1.07 2.613.03 2.63 2.38 2.71 3.14 3.02 maximum value 4.28 3.89 4.59 3.82 3.894.49 5.20 3.50 4.36 5.00 5.32 sample size 108 108 108 108 108 108 108108 108 108 108 Table A8-4 Pharmacophore Protein Distances Pharmacophoreelement O4 N2 H3 CA2 protein CYS_629 ARG_630 SER_657 GLY_656 MET_658SER_657 GLY_656 MET_658 SER_657 GLY_656 TYR_607 1  14 HA 3.52 HG3 2.07 O2.87 HA3 4.22 HE2 2.43 C 3.76 O 2.85 HE2 2.64 C 3.24 O 2.69 HD1 3.03 254_A HA 3.33 HG3 2.47 O 3.26 H 4.02 HA 3.15 C 3.88 O 3.02 HA 2.71 C 3.39O 2.85 HD2 3.18 3 54_B HA 3.33 HG3 2.47 O 3.26 H 4.02 HA 3.15 C 3.88 O3.02 HA 2.71 C 3.39 O 2.85 HD2 3.18 4 1129 HA 3.34 HG3 2.96 O 3.78 HA34.37 HA 4.00 HA 3.69 O 2.29 HA 3.51 C 3.36 O 2.22 HD1 3.07 5 1034 HA2.96 H 3.08 O 3.77 H 4.61 HA 3.53 O 3.57 O 2.48 HA 3.08 O 3.05 O 2.45HD1 3.62 6 1024 HA 3.41 H 2.89 O 3.50 H 4.14 HA 3.58 HA 3.63 O 2.60 HA3.08 C 3.24 O 2.52 HD1 2.64 7 1042_1 HA 3.29 H 3.78 O 3.35 H 4.33 HA3.93 C 3.73 O 2.75 HA 3.42 O 3.22 O 2.63 HA 4.32 8 1042_2 HA 3.66 H 3.71O 3.14 H 4.33 HG3 3.08 C 3.73 O 2.82 HG3 2.76 C 3.25 O 2.72 HA 4.49 91042_3 HA 2.98 H 3.09 O 4.14 H 4.91 HG3 3.30 HA 4.26 O 3.19 HG3 3.05 HA4.01 O 3.12 HA 4.90 10 2018 HA 3.45 H 3.08 O 3.75 H 4.25 N 3.81 C 3.93 O2.66 HA 3.29 C 3.47 O 2.50 HD1 3.42 11 1059 HA 3.18 HH11 2.69 O 3.68 H4.34 HA 3.60 O 3.79 O 2.65 HA 3.11 O 3.27 O 2.57 HD1 3.09 12 1088_A HA3.52 HG3 2.66 O 3.83 H 4.07 HA 3.94 O 3.77 O 2.69 HA 3.48 O 3.25 O 2.61HD1 3.32 13 1088_B HA 3.52 HG3 2.66 O 3.83 H 4.07 HA 3.94 O 3.77 O 2.69HA 3.48 O 3.25 O 2.61 HD1 3.32 14 1036_1 HA 3.20 HG3 2.93 O 3.69 H 4.06HA 3.87 HA 3.85 O 2.41 HA 3.38 C 3.44 O 2.28 HD1 3.46 15 1036_2_1 HA3.61 H 3.25 O 3.81 O 4.60 HA 3.61 HA 3.58 O 2.36 HA 3.11 C 3.26 O 2.25HD1 2.88 16 1036_2_2 HA 3.25 H 3.14 O 3.42 H 3.79 N 3.39 HA 3.50 O 2.42N 2.94 C 3.01 O 2.22 HD1 2.83 17 1081 HA 3.37 H 3.54 O 3.93 H 3.86 HA3.36 C 3.83 O 2.70 HA 2.91 C 3.40 O 2.61 HD2 3.75 18 1063 HA 3.50 HG32.82 O 3.73 H 3.80 HA 3.61 C 3.85 O 2.78 HA 3.10 C 3.39 O 2.69 HD1 4.5919 1065 HA 3.36 HG3 3.38 O 3.75 H 3.98 HA 3.71 C 3.97 O 2.82 HA 3.26 O3.50 O 2.68 HD1 4.13 20 1030_A HA 3.20 HG2 3.21 O 3.73 H 4.32 HA 3.69 C3.87 O 2.63 HA 3.17 C 3.42 O 2.49 HD1 3.30 21 1030_B HA 3.20 HG2 3.21 O3.73 H 4.32 HA 3.69 C 3.87 O 2.63 HA 3.17 C 3.42 O 2.49 HD1 3.30 22 1037HA 3.63 HB2 3.59 O 3.50 O 4.20 N 3.54 C 3.53 O 2.37 N 3.10 C 3.05 O 2.21HD1 2.93 23 1118 HA 3.27 HG3 2.89 O 3.70 H 4.20 SD 3.52 C 3.69 O 2.47 HA3.10 C 3.24 O 2.37 HD1 4.09 24 1090 HA 3.37 HG3 2.84 O 3.85 H 3.94 HA3.83 HA 3.80 O 2.53 HA 3.35 C 3.49 O 2.39 HD1 3.48 25 1007_1 HA 3.39 HG33.19 O 3.40 H 3.96 H 3.39 HA 3.87 O 2.69 H 3.03 C 3.46 O 2.53 HD1 3.3526 1007_2 HA 3.10 HH11 3.32 O 3.34 H 3.89 H 3.29 HA 3.95 O 3.07 H 2.90 C3.60 O 2.94 HD1 3.22 27 1149 HA 3.06 H 3.48 O 3.74 O 4.83 HA 3.24 C 4.09O 2.91 HA 2.75 C 3.65 O 2.79 HD1 3.48 28 1021_A HA 3.30 H 3.51 O 3.51 H3.81 HA 3.44 C 4.06 O 3.17 HA 2.94 C 3.59 O 3.07 HD1 2.94 29 1021_B HA3.30 H 3.52 O 3.52 H 3.80 HA 3.45 C 4.06 O 3.15 HA 2.95 C 3.58 O 3.05HD1 2.94 30 1097_1 HA 3.31 H 3.31 O 3.53 H 4.39 HA 3.67 C 3.60 O 2.41 HA3.19 C 3.14 O 2.30 HD1 3.48 31 1097_2 HA 3.24 H 3.15 O 3.67 H 4.21 HA3.56 C 3.72 O 2.48 HA 3.07 C 3.28 O 2.40 HD1 3.29 32 1031_1 HA 3.36 HD33.95 O 3.63 H 3.84 HA 3.47 C 4.09 O 3.13 HA 3.03 C 3.60 O 2.97 HD1 3.6633 1031_2 HA 3.42 H 4.08 O 3.62 H 3.80 HA 3.44 C 4.00 O 3.09 HA 3.03 C3.52 O 2.94 HD1 3.67 34 1031_3 HA 3.37 H 4.04 O 3.54 H 3.94 HA 3.33 C3.89 O 3.05 HA 2.92 C 3.41 O 2.91 HD1 3.37 35 1031_4 HA 3.42 H 3.89 O3.55 H 3.84 HA 3.32 C 3.87 O 3.05 HA 2.92 C 3.39 O 2.91 HD1 3.33 361153_A HA 3.36 HG2 3.01 O 3.58 H 4.16 HA 4.28 HA 3.90 O 2.59 HA 3.76 HA3.64 O 2.47 HD2 3.20 37 1153_B HA 3.36 HG2 3.01 O 3.58 H 4.16 HA 4.28 HA3.90 O 2.59 HA 3.76 HA 3.64 O 2.47 HD2 3.20 38 1025_1 HA 3.31 H 3.22 O3.58 HA3 4.23 HA 3.79 HA 3.97 O 2.86 HA 3.28 C 3.60 O 2.68 HD1 3.93 391025_2 HA 3.39 H 3.44 O 3.54 H 4.63 HA 3.43 C 4.10 O 2.83 HA 2.88 C 3.65O 2.72 HD1 3.78 40 1025_3 HA 3.32 H 3.39 O 4.38 HA3 3.88 H 2.96 HA 4.08O 3.00 H 2.63 C 3.77 O 2.86 HD2 3.57 41 1025_4 HA 3.44 HB3 3.18 O 4.07HA3 4.37 HA 3.27 C 4.23 O 2.74 HA 2.77 C 3.77 O 2.55 HD1 3.63 42 1025_5HA 3.05 H 2.73 O 3.87 H 4.15 HA 3.49 C 4.31 O 2.87 HA 3.00 C 3.85 O 2.62HD1 3.67 43 1025_6 HA 3.36 H 3.54 O 4.25 H 4.29 HA 3.40 HA 4.34 O 3.70HA 2.91 C 3.95 O 3.61 HD1 3.84 44 1089_A HA 3.50 H 3.11 O 3.81 H 4.04 HA3.94 HA 3.94 O 2.49 HA 3.46 C 3.51 O 2.32 HD1 3.59 45 1089_B HA 3.50 H3.11 O 3.81 H 4.04 HA 3.94 HA 3.94 O 2.49 HA 3.46 C 3.51 O 2.32 HD1 3.5946 1012_1 HA 3.15 HG3 3.06 O 3.75 H 3.78 HB2 3.60 C 4.31 O 2.92 HA 3.28C 3.82 O 2.71 HD1 4.05 47 1012_2 HA 3.28 HG3 3.28 O 3.61 H 3.74 H 3.91HA 3.98 O 2.63 N 3.51 HA 3.69 O 2.41 HD1 3.70 48 1078_1 HA 3.42 H 3.98 O3.63 H 3.72 H 3.54 C 3.92 O 2.79 H 3.22 C 3.43 O 2.65 HD1 3.63 491078_10 HA 3.33 HG2 3.27 O 3.79 H 3.88 H 3.63 C 3.95 O 2.94 HA 3.27 C3.47 O 2.82 HD1 3.77 50 1078_11 HA 3.42 H 3.97 O 3.62 H 3.72 H 3.51 HA3.90 O 2.78 H 3.18 C 3.42 O 2.63 HD1 3.52 51 1078_12 HA 3.43 HG2 3.48 O3.59 H 3.74 H 3.47 HA 3.84 O 2.73 H 3.15 C 3.36 O 2.59 HD1 3.47 521078_13 HA 3.42 HD3 3.52 O 3.63 H 3.73 H 3.52 HA 3.90 O 2.76 H 3.20 C3.41 O 2.62 HD1 3.55 53 1078_14 HA 3.42 HG2 3.33 O 3.59 H 3.76 H 3.48 C3.86 O 2.75 H 3.16 C 3.36 O 2.62 HD1 3.50 54 1078_15 HA 3.42 HG2 3.31 O3.60 H 3.73 H 3.47 HA 3.86 O 2.75 H 3.15 C 3.37 O 2.61 HD1 3.53 551078_16 HA 3.46 HD2 3.33 O 3.57 H 3.72 H 3.46 C 3.86 O 2.75 H 3.14 C3.36 O 2.62 HD1 3.53 56 1078_2 HA 3.40 HD2 3.28 O 3.56 H 3.74 H 3.49 HA3.85 O 2.71 H 3.15 C 3.40 O 2.57 HD1 3.56 57 1078_3 HA 3.30 HD2 3.18 O3.75 H 3.84 H 3.70 C 4.01 O 2.94 HA 3.30 C 3.53 O 2.80 HD1 3.89 581078_4 HA 3.42 HD2 3.36 O 3.57 H 3.71 H 3.49 HA 3.86 O 2.76 H 3.17 C3.38 O 2.61 HD1 3.52 59 1078_5 HA 3.43 HD2 3.26 O 3.59 H 3.71 H 3.48 HA3.89 O 2.76 H 3.16 C 3.40 O 2.62 HD1 3.53 60 1078_6 HA 3.45 HD2 3.23 O3.57 H 3.75 H 3.46 C 3.88 O 2.80 H 3.14 C 3.39 O 2.66 HD1 3.58 61 1078_7HA 3.42 HD3 3.55 O 3.62 H 3.72 H 3.54 C 3.91 O 2.78 H 3.21 C 3.42 O 2.64HD1 3.59 62 1078_8 HA 3.43 HD2 3.26 O 3.63 H 3.72 H 3.54 HA 3.88 O 2.74H 3.21 C 3.42 O 2.59 HD1 3.59 63 1078_9 HA 3.42 HD2 3.49 O 3.55 H 3.71 H3.42 HA 3.84 O 2.77 H 3.10 C 3.35 O 2.63 HD1 3.50 64 1145_A HA 3.25 HG33.08 O 3.64 H 3.95 N 4.03 HA 3.63 O 2.38 N 3.59 C 3.38 O 2.25 HD2 2.8765 1145_B HA 3.25 HG3 3.08 O 3.64 H 3.95 N 4.03 HA 3.63 O 2.38 N 3.59 C3.38 O 2.25 HD2 2.87 66 1050 HA 3.30 HG3 3.06 O 3.53 H 4.34 H 3.59 HA3.44 O 2.48 N 3.23 HA 3.21 O 2.43 HD1 3.00 67 1253 HA 3.22 HG3 3.03 O3.84 H 3.74 HA 3.69 C 4.30 O 2.96 HA 3.19 C 3.83 O 2.78 HD1 3.98 68 1257HA 3.27 HG3 3.28 O 3.83 H 3.78 HA 3.66 HA 3.89 O 2.64 HA 3.19 C 3.61 O2.43 HD1 3.56 69 999_1 HA 2.76 H 3.12 O 3.70 O 4.44 H 4.15 HA 3.47 O2.51 N 3.68 HA 3.22 O 2.36 HD2 3.10 70 999_2_A HA 3.38 HG3 2.63 O 3.77HA3 4.47 HA 3.98 HA 3.68 O 2.54 HA 3.50 HA 3.47 O 2.43 HD1 2.81 71999_2_B HA 3.38 HG3 2.63 O 3.77 HA3 4.47 HA 3.98 HA 3.68 O 2.54 HA 3.50HA 3.47 O 2.43 HD1 2.81 72 1297_1 HA 3.14 H 3.20 O 3.77 H 4.09 HA 3.86HA 4.01 O 2.79 HA 3.35 C 3.72 O 2.62 HD1 3.77 73 1297_2 HA 3.14 HG3 3.04O 3.77 H 4.04 HA 3.90 HA 3.99 O 2.76 HA 3.39 C 3.71 O 2.59 HD1 3.79 741297_3 HA 3.07 HG3 3.01 O 3.76 H 4.15 HA 3.76 HA 3.98 O 2.76 HA 3.26 C3.65 O 2.61 HD1 3.82 75 1297_4 HA 3.13 HG3 3.05 O 3.75 H 4.05 HA 3.88 HA3.95 O 2.70 HA 3.37 C 3.68 O 2.54 HD1 3.79 76 1297_5 HA 3.06 H 3.16 O3.80 H 4.13 HA 3.78 HA 3.99 O 2.75 HA 3.28 C 3.65 O 2.60 HD1 3.80 771297_6 HA 3.01 H 3.12 O 3.79 H 4.19 HA 3.75 HA 4.03 O 2.80 HA 3.26 C3.65 O 2.65 HD1 3.90 78 1304 HA 3.27 HG3 2.93 O 3.92 H 3.81 HA 3.83 C4.36 O 2.95 HA 3.31 C 3.89 O 2.75 HD1 4.00 79 1306_1 HA 3.75 H 3.46 O3.79 H 3.89 HA 3.82 C 4.00 O 2.18 HA 3.34 C 3.52 O 1.96 HD1 4.12 801306_2 HA 3.37 H 3.17 O 3.88 H 4.08 HA 4.20 HA 4.39 O 2.46 HA 3.70 C3.97 O 2.15 HD1 4.64 81 1307 HA 3.52 HG2 2.95 O 3.97 H 3.74 HA 4.06 O4.48 O 3.25 HA 3.63 O 3.97 O 3.07 HD1 4.00 82 1328_1 HA 3.26 HG3 3.02 O3.65 H 3.55 HA 3.70 C 4.35 O 2.97 HA 3.18 C 3.87 O 2.76 HD2 3.99 831328_2 HA 3.19 HG3 2.89 O 3.69 H 3.59 HE2 3.57 C 4.32 O 3.02 HA 3.12 C3.84 O 2.82 HD2 4.05 84 1328_3 HA 3.30 HG3 3.03 O 3.61 H 3.61 HA 3.76 C4.29 O 2.89 HA 3.24 C 3.81 O 2.69 HD2 3.90 85 1328_4 HA 3.19 HG3 3.07 O3.66 H 3.64 HA 3.72 C 4.26 O 2.86 HA 3.21 C 3.79 O 2.66 HD2 3.90 86 1334HA 3.27 HG3 2.93 O 3.85 H 4.11 HA 3.88 HA 4.07 O 2.79 HA 3.40 C 3.74 O2.61 HD1 4.28 87 1335 HA 3.28 HG3 2.85 O 3.55 H 4.09 HA 3.83 C 3.86 O2.56 HA 3.32 C 3.40 O 2.44 HD1 3.23 88 1338 HA 3.20 HG3 3.33 O 3.77 H3.71 HA 3.79 C 4.19 O 2.94 HA 3.28 C 3.71 O 2.74 HD1 4.20 89 1345_1 HA3.49 H 3.77 O 3.80 H 3.65 N 3.96 HA 3.83 O 2.41 N 3.52 C 3.48 O 2.25 HD13.39 90 1345_2 HA 2.92 N 3.67 O 4.00 H 4.19 HA 3.88 C 3.72 O 2.36 HA3.41 O 3.27 O 2.31 HD1 3.03 91 1351 HA 3.14 HG3 3.09 O 3.78 H 3.76 HG33.72 C 4.21 O 2.93 HA 3.24 C 3.74 O 2.79 HD1 3.83 92 1353 HA 3.28 HG33.00 O 3.95 H 3.69 HA 4.11 C 4.56 O 3.00 HA 3.60 C 4.09 O 2.77 HD1 4.4193 1367 HA 3.23 HG3 3.13 O 4.03 H 3.69 HG2 2.27 C 4.53 O 3.03 HG2 2.06 C4.05 O 2.80 HD1 3.69 94 1371 HA 3.36 HA 4.57 O 3.59 HA3 4.44 HA 3.59 HA3.81 O 2.95 HA 3.14 C 3.36 O 2.83 HD1 3.51 95 1372_A HA 3.20 HG3 2.85 O3.93 H 3.76 HA 3.91 C 4.44 O 2.93 HA 3.40 C 3.96 O 2.72 HD1 3.92 961372_B HA 3.20 HG3 2.86 O 3.94 H 3.76 HA 3.91 C 4.43 O 2.93 HA 3.40 C3.96 O 2.72 HD1 3.92 97 1373 HA 3.18 HG3 2.92 O 3.93 H 3.67 HA 3.90 C4.42 O 2.96 HA 3.38 C 3.94 O 2.76 HD1 4.03 98 1492 HA 3.48 H 3.16 O 3.65H 4.12 HA 3.54 O 3.69 O 2.40 HA 3.07 O 3.17 O 2.27 HD2 4.06 99 1399 HA3.21 HG3 2.96 O 3.93 H 3.69 HA 3.86 C 4.42 O 2.97 HA 3.35 C 3.95 O 2.77HD1 4.09 100 1360 HA 3.26 HG3 3.03 O 3.94 H 3.86 HA 3.91 C 4.45 O 2.99HA 3.40 C 3.98 O 2.77 HD1 4.08 101 1368 HA 3.36 HG3 2.92 O 3.99 H 3.82HA 4.04 C 4.58 O 2.94 HA 3.54 C 4.11 O 2.71 HD1 3.53 102 1406 HA 3.29 H3.40 O 3.93 H 3.88 HA 3.90 C 4.45 O 3.03 HA 3.38 C 3.98 O 2.85 HD1 4.28103 1411 HA 3.28 HG3 3.33 O 3.98 H 3.73 H 4.04 C 4.48 O 2.89 HA 3.53 C4.01 O 2.71 HD1 4.05 104 1433 HA 3.33 HG3 2.84 O 3.93 H 3.74 HA 3.98 C4.25 O 2.74 HA 3.48 C 3.78 O 2.55 HD1 3.65 105 1441 HA 3.22 HG3 3.22 O3.92 H 3.73 HA 3.83 C 4.39 O 2.99 HA 3.32 C 3.92 O 2.80 HD1 4.05 1061435 HA 3.19 HG3 3.00 O 3.92 H 3.79 HA 3.79 C 4.38 O 2.96 HA 3.28 C 3.91O 2.77 HD1 4.02 107 1450_A HA 3.35 HG3 2.92 O 3.89 H 3.74 HA 4.01 C 4.48O 2.89 HA 3.52 C 4.01 O 2.66 HD1 3.48 108 1450_B HA 3.35 HG3 2.92 O 3.89H 3.74 HA 4.01 C 4.48 O 2.89 HA 3.52 C 4.01 O 2.66 HD1 3.48 averagedistance 3.31 3.19 3.72 3.99 3.66 3.99 2.77 3.22 3.56 2.62 3.62 standarddeviation 0.16 0.37 0.21 0.29 0.32 0.28 0.24 0.27 0.27 0.24 0.44 minimumvalue 2.76 2.07 2.87 3.55 2.27 3.44 2.18 2.06 3.01 1.96 2.64 maximumvalue 3.75 4.57 4.38 4.91 4.28 4.58 3.70 3.76 4.11 3.61 4.90 sample size108 108 108 108 108 108 108 108 108 108 108 Table A8-5 Pharmacophoreprotein distances Pharmacophore element CA2 CA4 C2 C4 CA5 proteinPHE_529 PRO_608 PHE_529 PRO_608 GLY_528 TYR_607 GLY_656 TRP_655 PRO_608TYR_607 1  14 HE2 2.94 HD2 4.26 HE2 4.38 HD2 4.56 HA2 3.16 HE1 2.86 O3.61 HE3 4.07 HD2 4.18 HD1 3.14 2 54_A HE1 3.38 HD2 4.39 HE1 4.32 HD24.90 HA2 3.15 HE2 2.87 O 3.79 HE3 4.07 HD2 4.49 HE2 3.00 3 54_B HE1 3.38HD2 4.39 HE1 4.32 HD2 4.90 HA2 3.15 HE2 2.87 O 3.79 HE3 4.07 HD2 4.49HE2 3.00 4 1129 HE1 3.21 HD2 4.10 HE1 3.86 HD3 4.02 H 3.14 HE1 3.29 O2.92 HE3 3.81 HD3 3.42 HE1 3.36 5 1034 HE2 3.60 HD2 2.94 HE2 4.03 HG32.99 HA2 3.44 HE1 3.89 O 2.94 HE3 3.65 HD3 2.64 HD1 3.48 6 1024 HE1 3.52HD2 3.77 HE1 3.82 HD2 3.65 H 3.12 HE1 2.95 O 3.18 HE3 3.90 HD3 3.31 HE12.98 7 1042_1 HD1 3.81 HD3 3.44 HE1 3.31 HG3 3.20 HA2 3.24 HE1 4.35 O3.48 HE3 4.01 HD3 3.09 HD1 3.65 8 1042_2 HE1 3.48 HD3 3.39 HE1 3.82 HG33.28 H 3.09 HE1 4.29 O 3.46 HE3 3.77 HD3 3.24 HD1 3.63 9 1042_3 HE2 2.72HD3 4.05 HE2 3.89 HG3 3.61 H 2.24 HE2 5.63 O 3.58 HE3 3.94 HG3 3.32 HA4.32 10 2018 HE2 3.04 HD2 3.81 HE2 3.94 HG2 3.94 HA2 3.15 HE1 3.54 O3.43 HE3 4.05 HD3 3.64 HD1 3.62 11 1059 HE2 3.22 HD2 3.66 HE2 4.14 HG23.10 HA2 3.15 HE1 3.27 O 3.20 HE3 3.81 HD3 3.03 HD1 3.27 12 1088_A HE12.77 HD2 3.83 HE1 3.63 HG2 3.79 H 3.31 HE3 3.54 O 3.22 HE3 4.01 HD3 3.53HD1 3.51 13 1088_B HE1 2.77 HD2 3.83 HE1 3.63 HG2 3.79 H 3.31 HE1 3.54 O3.22 HE3 4.01 HD3 3.53 HD1 3.51 14 1036_1 HE1 3.13 HD2 4.04 HE1 3.80 HD24.18 H 3.25 HE1 3.64 O 3.16 HE3 3.75 HD3 3.85 HD1 3.68 15 1036_2_1 HE13.34 HD2 4.07 HE1 4.10 HD2 3.86 H 3.18 HE1 3.26 O 3.07 HE3 3.89 HD2 3.64HD1 3.12 16 1036_2_2 HE1 3.42 HD2 4.28 HE1 4.30 HD2 4.07 H 2.86 HE1 3.11O 3.35 HE3 3.66 HD2 3.81 HD1 2.74 17 1081 HE1 3.38 HD2 4.75 HE1 3.76 HG34.86 H 3.04 HE2 3.60 O 3.27 HE3 4.23 HD2 4.41 HE2 3.60 18 1063 HE1 3.14HD2 4.82 HE1 3.65 HG3 5.00 H 2.88 HE1 4.25 O 3.33 HE3 4.09 HG3 4.68 HD14.11 19 1065 HE2 2.79 HD2 3.59 HE2 3.73 HG3 3.28 HA2 3.22 HE1 3.99 O3.46 HE3 3.81 HG3 3.07 HD1 3.92 20 1030_A HE2 3.07 HD2 3.42 HE2 3.88 HG23.09 HA2 3.11 HE1 3.45 O 3.33 HE3 3.79 HD3 3.20 HD1 3.32 21 1030_B HE23.07 HD2 3.42 HE2 3.88 HG2 3.09 HA2 3.11 HE1 3.45 O 3.33 HE3 3.79 HD33.20 HD1 3.32 22 1037 HE1 3.61 HD2 4.28 HE1 4.25 HD2 4.28 H 3.32 HE13.12 O 3.26 HE3 3.58 HD3 3.98 HD1 3.14 23 1118 HE1 3.15 HD2 4.98 HE13.49 HG2 5.23 HA2 3.39 HE1 4.10 O 3.12 HE3 4.09 HD2 4.99 HD1 4.06 241090 HE2 2.91 HD2 4.04 HE2 3.93 HG2 4.11 HA2 3.24 HE1 3.54 O 3.25 HE33.71 HD3 4.04 HE1 3.67 25 1007_1 HE1 3.36 HD2 2.45 HE1 4.14 HG3 2.40 H3.49 HE1 3.19 O 3.49 HE3 3.81 HD3 2.21 HD1 2.89 26 1007_2 HE1 3.32 HD22.40 HE1 3.92 HG2 2.08 H 3.40 HE1 3.11 O 3.69 HE3 3.85 HG2 2.22 HD1 3.0927 1149 HE2 3.05 HD2 4.16 HE2 4.04 HD2 4.51 H 3.41 HE1 3.01 O 3.52 HE33.66 HD2 4.06 HD1 2.46 28 1021_A HE1 3.11 HD2 3.41 HE1 4.06 HG3 3.26 H2.95 HE1 2.90 O 3.70 HE3 4.07 HD3 2.84 HD1 3.09 29 1021_B HE1 3.10 HD23.43 HE1 4.05 HG3 3.27 H 2.94 HE1 2.90 O 3.68 HE3 4.06 HD3 2.86 HD1 3.0830 1097_1 HE1 3.14 HD2 3.88 HE1 3.98 HG2 3.91 HA2 3.20 HE1 3.53 O 3.12HE3 3.52 HD3 3.72 HD1 3.41 31 1097_2 HE1 2.91 HD2 3.71 HE1 3.72 HD3 3.71H 3.06 HE1 3.49 O 3.09 HE3 3.42 HD3 3.25 HD1 3.08 32 1031_1 HE1 3.16 HD23.05 HE1 3.76 HG3 3.31 H 3.19 HE1 3.28 O 3.80 HE3 3.94 HG3 3.07 HD1 3.5033 1031_2 HE1 3.22 HD2 3.02 HE1 3.82 HG3 3.30 H 3.20 HE1 3.26 O 3.77 HE33.92 HG3 3.06 HD1 3.48 34 1031_3 HE1 3.17 HD2 3.00 HE1 3.76 HG3 3.40 H3.26 HE1 3.02 O 3.71 HE3 3.96 HD2 3.02 HD1 3.19 35 1031_4 HE1 3.17 HD22.97 HE1 3.73 HG3 3.35 H 3.19 HE1 2.99 O 3.73 HE3 3.96 HD2 2.96 HD1 3.1636 1153_A HE1 3.32 HD2 4.47 HE1 3.44 HD2 4.63 H 3.05 HE2 3.20 O 3.28 HE33.87 HD3 4.25 HE2 3.01 37 1153_B HE1 3.32 HD2 4.47 HE1 3.44 HD2 4.63 H3.05 HE2 3.20 O 3.28 HE3 3.87 HD3 4.25 HE2 3.01 38 1025_1 HE2 3.64 HD33.34 HE2 4.56 HG2 2.96 H 2.73 HE1 4.04 O 3.63 HE3 3.88 HG2 3.00 HD1 3.7439 1025_2 HE1 2.81 HD2 3.22 HE1 3.42 HG2 2.83 H 2.80 HE1 4.15 O 3.46 HE34.18 HG2 2.95 HD1 4.05 40 1025_3 HE1 3.08 HD2 3.55 HE1 3.98 HG3 3.68 H2.83 HE2 3.72 O 3.63 HE3 3.87 HD2 3.18 HD2 3.20 41 1025_4 HE2 2.85 HD24.23 HE2 4.08 HG2 3.44 H 2.77 HE1 3.56 O 3.54 HE3 3.80 HG2 3.26 HD1 3.2742 1025_5 HE2 3.18 HD2 3.65 HE2 4.21 HG3 3.37 H 3.01 HE1 3.85 O 3.81 HE34.00 HG3 3.25 HD1 3.62 43 1025_6 HE1 3.04 HD2 3.19 HE1 4.13 HG3 3.07 H2.68 HE1 3.43 O 4.09 HE3 3.96 HG3 2.97 HD1 3.37 44 1089_A HE2 2.87 HD24.07 HE2 3.84 HD2 4.23 H 3.25 HE1 3.73 O 3.27 HE3 3.71 HD3 3.81 HD1 3.7845 1089_B HE2 2.87 HD2 4.07 HE2 3.84 HD2 4.23 H 3.25 HE1 3.73 O 3.27 HE33.71 HD3 3.81 HD1 3.78 46 1012_1 HE2 2.84 HD2 3.82 HE2 4.04 HG3 3.88 H3.04 HE1 3.95 O 3.77 HE3 3.91 HG3 3.66 HD1 3.92 47 1012_2 HE1 3.02 HD23.59 HE1 3.93 HG3 3.86 HA2 3.24 HE1 3.49 O 3.57 HE3 3.67 HG3 3.62 HD13.49 48 1078_1 HE1 3.36 HD2 2.94 HE1 4.01 HG3 2.83 HA2 3.32 HE1 3.67 O3.52 HE3 3.86 HG3 2.68 HD1 3.41 49 1078_10 HE1 3.14 HD2 2.98 HE1 3.87HG3 2.80 H 3.33 HE1 3.93 O 3.57 HE3 4.02 HG3 2.70 HD1 3.68 50 1078_11HE1 3.41 HD2 2.72 HE1 4.04 HG3 2.52 HA2 3.33 HE1 3.61 O 3.51 HE3 3.91HG3 2.42 HD1 3.35 51 1078_12 HE1 3.50 HD2 2.86 HE1 4.08 HG3 2.76 HA23.39 HE1 3.56 O 3.46 HE3 3.87 HG3 2.65 HD1 3.32 52 1078_13 HE1 3.37 HD22.83 HE1 4.00 HG3 2.64 HA2 3.35 HE1 3.64 O 3.50 HE3 3.90 HG3 2.54 HD13.38 53 1078_14 HE1 3.45 HD2 2.78 HE1 4.03 HG3 2.63 HA2 3.39 HE1 3.56 O3.46 HE3 3.85 HG3 2.54 HD1 3.29 54 1078_15 HE1 3.43 HD2 2.76 HE1 4.05HG3 2.55 HA2 3.40 HE1 3.59 O 3.48 HE3 3.90 HG3 2.43 HD1 3.32 55 1078_16HE1 3.44 HD2 2.91 HE1 4.05 HG3 2.80 HA2 3.39 HE1 3.59 O 3.47 HE3 3.87HG3 2.68 HD1 3.36 56 1078_2 HE1 3.44 HD2 2.86 HE1 4.03 HG3 2.75 HA2 3.37HE1 3.61 O 3.46 HE3 3.85 HG3 2.60 HD1 3.36 57 1078_3 HE1 3.16 HD2 3.06HE1 3.88 HG3 2.91 HA2 3.26 HE1 3.96 O 3.60 HE3 3.98 HG3 2.67 HD1 3.70 581078_4 HE1 3.47 HD2 2.84 HE1 4.04 HG3 2.79 HA2 3.42 HE1 3.55 O 3.50 HE33.86 HG3 2.65 HD1 3.33 59 1078_5 HE1 3.44 HD2 2.75 HE1 4.06 HG3 2.62 HA23.36 HE1 3.58 O 3.51 HE3 3.87 HG3 2.50 HD1 3.34 60 1078_6 HE1 3.45 HD22.81 HE1 4.02 HG3 2.70 HA2 3.40 HE1 3.63 O 3.52 HE3 3.86 HG3 2.54 HD13.37 61 1078_7 HE1 3.39 HD2 2.92 HE1 4.03 HG3 2.81 HA2 3.35 HE1 3.65 O3.52 HE3 3.89 HG3 2.68 HD1 3.40 62 1078_8 HE1 3.42 HD2 2.78 HE1 4.03 HG32.66 HA2 3.35 HE1 3.64 O 3.49 HE3 3.84 HG3 2.49 HD1 3.38 63 1078_9 HE13.49 HD2 2.80 HE1 4.07 HG3 2.64 HA2 3.41 HE1 3.56 O 3.51 HE3 3.90 HG32.53 HD1 3.34 64 1145_A HE1 3.84 HD2 4.06 HE1 3.74 HD2 4.32 HA2 3.39 HE22.78 O 3.15 HE3 3.98 HD2 3.93 HE2 3.11 65 1145_B HE1 3.84 HD2 4.06 HE13.74 HD2 4.32 HA2 3.39 HE2 2.78 O 3.15 HE3 3.98 HD2 3.93 HE2 3.11 661050 HE1 3.44 HD2 3.89 HE1 3.59 HD2 4.18 H 2.83 HE1 2.83 O 3.03 HE3 3.86HD2 3.84 HD1 3.17 67 1253 HE1 2.82 HD2 3.85 HE1 3.65 HG2 3.80 HA2 3.20HE1 4.06 O 3.72 HE3 4.09 HD3 3.72 HD1 4.14 68 1257 HE1 3.01 HD2 4.22 HE13.94 HD2 4.26 HA2 3.22 HE1 3.71 O 3.51 HE3 3.82 HD3 3.95 HD1 3.91 69999_1 HE1 3.35 HD2 3.47 HE1 4.36 HD2 3.51 HA2 3.53 HE2 3.18 O 3.30 HE33.73 HD2 3.11 HD2 2.83 70 999_2_A HE2 3.51 HD2 3.50 HE2 4.26 HG3 3.50 H3.42 HE1 2.82 O 3.22 HE3 3.77 HD3 3.21 HD1 2.69 71 999_2_B HE2 3.51 HD23.50 HE2 4.26 HG3 3.50 H 3.42 HE1 2.82 O 3.22 HE3 3.77 HD3 3.21 HD1 2.6972 1297_1 HE2 2.80 HD2 3.25 HE2 3.89 HG3 3.22 H 3.05 HE1 3.78 O 3.55 HE33.76 HG3 3.10 HD1 3.39 73 1297_2 HE2 2.83 HD2 3.33 HE2 3.90 HG3 3.36 H3.11 HE1 3.80 O 3.53 HE3 3.69 HG3 3.23 HD1 3.41 74 1297_3 HE2 2.73 HD23.38 HE2 3.84 HG3 3.40 H 3.05 HE1 3.83 O 3.50 HE3 3.79 HG3 3.29 HD1 3.4775 1297_4 HE2 2.84 HD2 3.35 HE2 3.91 HG3 3.38 H 3.11 HE1 3.79 O 3.48 HE33.66 HG3 3.24 HD1 3.41 76 1297_5 HE2 2.84 HD2 3.38 HE2 3.90 HG3 3.38 H3.09 HE1 3.86 O 3.47 HE3 3.74 HG3 3.29 HD1 3.43 77 1297_6 HE2 2.73 HD23.48 HE2 3.85 HG3 3.55 H 3.03 HE1 3.91 O 3.51 HE3 3.79 HG3 3.43 HD1 3.5378 1304 HE2 2.73 HD2 3.25 HE2 3.87 HG2 2.79 HA2 3.20 HE1 4.02 O 3.74 HE33.98 HG2 2.73 HD1 4.07 79 1306_1 HE1 3.11 HG2 3.29 HE1 3.94 HG3 2.57 HA22.95 HE1 3.72 O 3.14 HE3 3.09 HG3 2.23 HD1 3.02 80 1306_2 HE2 3.44 HD23.54 HE2 4.76 HG2 3.21 HA2 2.72 HE1 4.24 O 3.54 HE3 3.30 HG2 2.86 HD13.57 81 1307 HE2 2.96 HD2 3.31 HE2 4.24 HG2 2.81 HA2 3.07 HE1 3.85 O3.92 HE3 4.14 HG2 2.74 HD1 4.09 82 1328_1 HE1 3.00 HD2 3.11 HE1 4.14 HG33.10 H 3.53 HE2 3.81 O 3.82 HE3 3.99 HG3 2.66 HD2 3.75 83 1328_2 HE13.01 HD2 3.23 HE1 4.18 HG3 3.19 H 3.51 HE2 3.90 O 3.84 HE3 4.05 HG3 2.76HD2 3.84 84 1328_3 HE1 2.93 HD2 3.01 HE1 4.03 HG2 2.99 H 3.51 HE2 3.78 O3.75 HE3 3.96 HG3 2.65 HD2 3.60 85 1328_4 HE1 2.89 HD2 3.12 HE1 3.99 HG33.11 H 3.54 HE2 3.79 O 3.70 HE3 3.94 HG3 2.77 HD2 3.63 86 1334 HE2 2.49HD2 3.91 HE2 3.69 HG3 3.70 HA2 3.42 HE1 4.17 O 3.57 HE3 4.13 HG3 3.44HD1 4.06 87 1335 HE1 3.17 HD2 4.16 HE1 3.69 HD2 4.39 HA2 3.18 HE1 3.16 O3.21 HE3 3.88 HD2 4.01 HD1 3.33 88 1338 HE2 2.66 HD2 3.77 HE2 4.01 HG33.91 HA2 3.20 HE1 4.09 O 3.72 HE3 3.88 HG3 3.68 HD1 4.08 89 1345_1 HE23.45 HD2 3.25 HE2 4.32 HG3 2.93 HA2 2.86 HE1 3.20 O 3.22 HE3 3.72 HD22.66 HD1 2.73 90 1345_2 HE1 3.30 HD2 3.50 HE1 3.92 HG3 3.60 HA2 3.53 HE13.36 O 2.95 HE3 3.74 HD3 3.13 HD1 3.06 91 1351 HE1 2.79 HD2 4.25 HE13.82 HG2 4.52 HA2 3.32 HE1 3.79 O 3.64 HE3 3.90 HD3 4.24 HD1 4.03 921353 HE2 2.90 HD2 3.12 HE2 3.96 HG2 2.70 HA2 3.25 HE1 4.37 O 3.85 HE33.93 HG2 2.45 HA 4.28 93 1367 HE2 2.76 HD2 3.76 HE2 3.91 HG2 3.65 HA23.09 HE1 3.75 O 3.91 HE3 4.02 HD3 3.47 HD1 3.78 94 1371 HE2 2.97 HD23.45 HE2 3.91 HG3 3.53 H 2.83 HE1 3.48 O 3.59 HE3 4.26 HD3 3.22 HD1 3.6495 1372_A HE2 2.79 HD2 3.18 HE2 3.94 HG2 2.75 HA2 3.15 HE1 3.95 O 3.76HE3 4.00 HG2 2.70 HD1 4.04 96 1372_B HE2 2.79 HD2 3.18 HE2 3.94 HG2 2.75HA2 3.15 HE1 3.94 O 3.75 HE3 3.99 HG2 2.70 HD1 4.04 97 1373 HE2 2.71 HD23.39 HE2 3.89 HG2 2.98 HA2 3.15 HE1 4.02 O 3.77 HE3 4.03 HG2 2.98 HD14.09 98 1492 HD1 3.54 HD2 3.74 HE1 3.79 HG3 3.93 HA2 2.98 HE2 4.07 O3.17 HE3 3.52 HD3 3.67 HD2 4.11 99 1399 HE2 2.74 HD2 3.85 HE2 3.77 HG23.83 HA2 3.17 HE1 4.09 O 3.77 HE3 4.14 HD3 3.70 HD1 4.30 100 1360 HE22.83 HD2 4.28 HE2 3.87 HG3 4.66 HA2 3.14 HE1 4.00 O 3.83 HE3 3.84 HG34.46 HD1 4.18 101 1368 HE1 3.40 HD2 4.44 HE1 3.45 HD2 4.58 HA2 3.26 HE13.47 O 3.80 HB2 4.32 HD3 4.09 HE1 3.74 102 1406 HE2 2.66 HD2 3.44 HE23.81 HG2 3.12 HA2 3.08 HE1 4.29 O 3.80 HE3 4.00 HG2 2.99 HD1 4.37 1031411 HE2 3.01 HD2 3.26 HE2 3.59 HG3 3.06 H 3.04 HE1 4.13 O 3.66 HE3 4.01HG3 3.01 HD1 4.12 104 1433 HE2 3.01 HD2 4.25 HE2 3.58 HD2 4.45 HA2 3.20HE1 3.81 O 3.57 HE3 4.04 HD3 4.14 HD1 3.87 105 1441 HE2 3.02 HD2 3.61HE2 3.59 HG2 3.23 HA2 3.18 HE1 4.16 O 3.74 HE3 4.13 HG2 3.24 HD1 4.05106 1435 HE2 2.82 HD2 3.90 HE2 3.87 HG2 3.87 HA2 3.08 HE1 4.06 O 3.73HE3 3.98 HD3 3.60 HD1 4.12 107 1450_A HE2 2.97 HD2 4.02 HE2 3.67 HG24.21 HA2 3.20 HE1 3.62 O 3.77 HE3 4.10 HD3 3.84 HE1 4.03 108 1450_B HE22.97 HD2 4.02 HE2 3.67 HG2 4.21 HA2 3.20 HE1 3.62 O 3.77 HE3 4.10 HD33.84 HE1 4.03 average distance 3.14 3.56 3.92 3.51 3.18 3.62 3.50 3.893.28 3.52 standard deviation 0.30 0.55 0.24 0.68 0.21 0.45 0.25 0.190.61 0.42 minimum value 2.49 2.40 3.31 2.08 2.24 2.78 2.92 3.09 2.212.46 maximum value 3.84 4.98 4.76 5.23 3.54 5.63 4.09 4.32 4.99 4.37sample size 108 108 108 108 108 108 108 108 108 108 Table A8-6Pharmacophore protein distances Pharmacophore element C6 CA3 O3 H1protein TRP_655 PHE_529 SER_611 PRO_608 GLY_528 MET_658 ARG_630 ARG_630MET_658 1  14 CH2 3.76 HD2 2.77 HB3 2.64 HD2 4.32 HA2 3.51 O 2.13 HH111.53 HH12 2.47 HG2 3.80 2 54_A CH2 3.90 HD1 2.99 HB3 2.76 HD2 4.34 HA23.70 O 2.38 HD3 1.88 HH12 2.44 HG2 3.80 3 54_B CH2 3.90 HD1 2.99 HB32.76 HD2 4.34 HA2 3.70 O 2.38 HD3 1.88 HH12 2.44 HG2 3.80 4 1129 CZ33.31 HD1 2.98 HB3 2.58 HD2 4.05 HA2 3.51 HG2 2.85 HD2 2.14 HD2 3.63 HE33.11 5 1034 CZ3 3.27 HD2 3.09 OG 3.32 HD2 2.97 HA2 3.79 HG2 2.86 HD24.27 HH11 3.41 HG2 3.46 6 1024 CH2 3.53 HD1 3.20 HB3 2.54 HD2 3.95 HA23.60 HG2 1.94 HD3 3.62 HH11 3.35 HG2 3.26 7 1042_1 CZ3 3.28 HD1 3.84 HB32.14 HD2 3.46 HA2 4.67 HG2 2.06 HB2 4.52 HH11 4.01 SD 3.40 8 1042_2 CZ33.27 HD1 3.09 HB3 2.54 HD2 3.74 HA2 4.01 HG2 1.07 HB2 5.37 HD2 5.65 HG24.17 9 1042_3 CZ3 3.21 HD2 2.42 HB3 2.32 HD2 4.06 HA2 2.99 HG2 2.74 HD24.10 HD2 4.10 HG2 4.20 10 2018 CH2 3.77 HD2 2.90 HB3 2.86 HD2 3.74 HA23.65 HG2 1.58 HB2 4.11 HH22 5.01 SD 2.86 11 1059 CZ3 3.64 HD2 2.97 HB32.61 HD2 3.70 HA2 3.81 SD 1.94 CZ 2.01 HH21 3.32 HE2 0.74 12 1088_A CH23.75 HD1 2.75 HB3 2.71 HD2 3.74 HA2 3.66 HG3 3.04 NH1 2.33 HE 3.72 HE23.12 13 1088_B CH2 3.75 HD1 2.75 HB3 2.71 HD2 3.74 HA2 3.66 HG3 3.04 NH12.33 HE 3.72 HE2 3.12 14 1036_1 CH2 3.49 HD1 2.97 HB3 2.82 HD2 3.87 HA23.62 HG2 2.89 HH11 1.75 HH22 2.82 HG2 3.32 15 1036_2_1 CZ3 3.43 HD1 3.12HB3 2.69 HD2 4.19 HA2 3.51 HG3 1.86 HD3 3.64 HH11 3.13 SD 2.42 161036_2_2 CH2 3.51 HD1 3.09 HB3 2.65 HD2 4.42 HA2 3.26 HG2 2.14 HB2 4.14HH11 3.90 SD 2.62 17 1081 CZ3 3.69 HD1 3.23 HB3 2.66 HG2 4.72 HA2 3.22HG3 3.11 HD3 4.09 HH11 3.97 HG2 3.70 18 1063 CZ3 3.73 HD1 3.00 HB3 3.00HG2 4.92 HA2 3.37 HG2 1.74 HD2 2.08 HH11 2.64 SD 2.75 19 1065 CH2 3.87HD2 2.70 HB3 2.57 HD2 3.75 HA2 3.56 O 3.34 HD2 2.94 HD3 4.01 HE3 3.79 201030_A CZ3 3.63 HD2 2.90 HB3 2.90 HD2 3.66 HA2 3.77 HB2 3.11 HD2 3.07HD3 4.19 HG3 3.33 21 1030_B CZ3 3.63 HD2 2.90 HB3 2.90 HD2 3.66 HA2 3.77HB2 3.11 HD2 3.07 HD3 4.19 HG3 3.33 22 1037 CH2 3.29 HD1 3.25 HB3 2.19HD2 4.17 HA2 3.46 HG3 2.38 HH11 3.02 HH12 2.95 HG3 3.03 23 1118 CZ3 3.71HD1 3.01 HB3 3.12 HD2 4.83 HA2 3.82 HE3 1.45 HH11 2.14 HH21 3.05 HE23.28 24 1090 CH2 3.50 HD2 2.77 HB3 2.87 HD2 3.95 HA2 3.61 HG3 2.69 HE1.87 HH21 2.38 HE2 2.71 25 1007_1 CH2 3.70 HD1 3.15 HB3 2.06 HD2 3.15HA2 3.76 HA 2.61 NH1 2.01 HH21 3.34 HG2 3.25 26 1007_2 CH2 3.60 HD1 3.20HB3 2.21 HD2 3.12 HA2 3.72 HA 2.59 NH1 2.20 NE 3.80 HG3 3.37 27 1149 CZ33.27 HD2 2.93 HB3 2.96 HD2 4.39 HA2 3.92 HG2 2.55 HB2 4.48 HH11 4.24 SD3.25 28 1021_A CZ3 3.96 HD1 2.91 HB3 2.27 HD2 3.43 HA2 3.58 HG2 2.19 HB24.48 HD2 5.78 SD 3.50 29 1021_B CZ3 3.95 HD1 2.90 HB3 2.27 HD2 3.45 HA23.59 HG2 2.20 HB2 4.47 HD2 5.77 SD 3.50 30 1097_1 CZ3 3.24 HD1 2.89 HB33.04 HD2 3.89 HA2 3.46 HG2 2.40 HH11 3.62 HH11 2.96 HG2 3.49 31 1097_2CZ3 3.09 HD1 3.02 HB3 3.29 HD2 3.56 HA2 3.52 HG2 2.55 HH11 3.42 HH123.06 SD 3.13 32 1031_1 CH2 3.81 HD1 3.12 HB3 2.09 HD2 3.68 HA2 3.40 O3.12 HD3 3.31 HH11 4.78 HG2 4.43 33 1031_2 CH2 3.80 HD1 3.14 HB3 2.00HD2 3.67 HA2 3.46 O 3.02 HD2 3.25 HD2 4.71 O 4.44 34 1031_3 CH2 3.77 HD13.16 HB3 2.21 HD2 3.52 HA2 3.51 O 2.96 HD2 3.12 HH21 4.69 O 4.41 351031_4 CH2 3.78 HD1 3.11 HB3 2.18 HD2 3.53 HA2 3.41 O 2.96 HD2 3.18 HD24.47 O 4.40 36 1153_A CH2 3.42 HD1 3.23 HB3 2.46 HD2 4.41 HA2 3.41 HG32.53 HG3 3.85 HG3 5.84 HG2 3.26 37 1153_B CH2 3.42 HD1 3.23 HB3 2.46 HD24.41 HA2 3.41 HG3 2.53 HG3 3.85 HG3 5.84 HG2 3.26 38 1025_1 CZ3 3.64 HD23.33 HB3 2.92 HD2 3.34 HA2 3.40 HG3 2.13 HD2 2.63 HD2 3.92 HG2 3.17 391025_2 CZ3 3.94 HD1 2.86 HB3 2.64 HD2 3.48 HA2 3.65 HG2 2.04 HD2 2.22HH11 2.23 HG2 3.76 40 1025_3 CZ2 3.77 HD1 3.29 HB3 3.99 HG2 3.92 HA23.28 HG2 2.77 HH22 0.15 HH12 2.66 HG2 3.75 41 1025_4 CZ3 4.11 HD2 2.69HB3 2.77 HG2 4.73 HA2 3.71 HG2 2.30 HD2 3.03 HH12 1.74 HG2 3.43 421025_5 CH2 3.83 HD2 2.96 HB3 3.26 HG2 4.19 HA2 3.45 HG2 2.64 HG3 3.76HH11 3.56 SD 3.27 43 1025_6 CZ2 4.08 HD1 2.99 HB3 2.70 HG2 3.50 HA2 3.01O 3.09 HD2 3.57 HD3 3.91 HG2 3.64 44 1089_A CH2 3.57 HD2 2.81 HB3 2.79HD2 3.90 HA2 3.59 HG3 2.61 HB3 4.55 HD2 5.31 HG3 3.31 45 1089_B CH2 3.57HD2 2.81 HB3 2.79 HD2 3.90 HA2 3.59 HG3 2.61 HB3 4.55 HD2 5.31 HG3 3.3146 1012_1 CZ2 3.91 HD2 2.66 HB3 3.15 HD2 4.17 HA2 3.39 HG3 1.78 HH212.09 HE 3.57 HG2 3.32 47 1012_2 CH2 3.61 HD1 2.98 HB3 2.57 HD2 3.98 HA23.69 HG2 1.87 HH11 1.95 NE 3.50 SD 3.25 48 1078_1 CH2 3.68 HD1 3.30 HB32.41 HD2 3.85 HA2 3.66 O 2.97 HD2 3.27 HD3 4.80 HG2 3.50 49 1078_10 CH23.89 HD1 3.08 HB3 2.78 HD2 3.66 HA2 3.40 O 3.04 HG3 3.67 HH12 4.55 HG23.81 50 1078_11 CH2 3.64 HD1 3.33 HB3 2.38 HD2 3.69 HA2 3.68 HA 3.00 HD23.33 HD2 4.87 HG2 3.71 51 1078_12 CH2 3.63 HD1 3.41 HB3 2.36 HD2 3.77HA2 3.71 O 2.95 HG3 3.99 HH12 5.01 HG2 3.50 52 1078_13 CH2 3.66 HD1 3.31HB3 2.46 HD2 3.75 HA2 3.63 HA 2.99 HH22 3.72 HH12 4.91 HG2 3.66 531078_14 CH2 3.60 HD1 3.36 HB3 2.33 HD2 3.74 HA2 3.63 O 2.94 HG3 3.85HH12 4.50 HG2 3.46 54 1078_15 CH2 3.62 HD1 3.35 HB3 2.34 HD2 3.75 HA23.65 O 2.92 HG3 3.82 HH12 4.35 HG2 3.44 55 I078_16 CH2 3.62 HD1 3.38 HB32.38 HD2 3.81 HA2 3.72 O 2.91 HD3 3.38 HH12 4.49 HG2 3.54 56 1078_2 CH23.62 HD1 3.35 HB3 2.35 HD2 3.80 HA2 3.67 HA 2.86 HD3 3.38 HH12 4.58 HG23.34 57 1078_3 CH2 3.85 HD1 3.07 HB3 2.66 HG2 3.81 HA2 3.42 O 3.08 HD33.18 HH12 4.30 HG2 3.79 58 1078_4 CH2 3.63 HD1 3.40 HB3 2.27 HD2 3.78HA2 3.71 O 2.91 HD3 3.43 HH22 4.75 HG2 3.41 59 1078_5 CH2 3.64 HD1 3.36HB3 2.31 HD2 3.70 HA2 3.70 O 2.94 HD3 3.42 HH22 4.78 HG2 3.52 60 1078_6CH2 3.64 HD1 3.36 HB3 2.29 HD2 3.75 HA2 3.71 O 2.91 HD3 3.39 HH12 4.89HG2 3.53 61 1078_7 CH2 3.70 HD1 3.31 HB3 2.46 HD2 3.81 HA2 3.67 O 2.92HH12 3.06 HH22 4.82 HG2 3.42 62 1078_8 CH2 3.66 HD1 3.34 HB3 2.31 HD23.76 HA2 3.68 HA 2.93 HD3 3.32 HH12 5.00 HG2 3.44 63 1078_9 CH2 3.64 HD13.40 HB3 2.41 HD2 3.75 HA2 3.70 O 2.86 HD3 3.54 HH22 5.17 HG2 3.48 641145_A CH2 3.75 HD1 3.57 HB3 2.78 HD2 4.21 HA2 3.65 HA 2.98 NE 2.66 HE2.55 HE2 3.20 65 1145_B CH2 3.75 HD1 3.57 HB3 2.78 HD2 4.21 HA2 3.65 HA2.98 NE 2.66 HE 2.55 HE2 3.20 66 1050 CH2 3.63 HD1 3.25 HB3 2.37 HD23.95 HA2 3.29 HE3 1.47 CZ 2.22 HH21 2.49 HE1 1.56 67 1253 CZ2 3.95 HD12.74 HB3 2.80 HD2 3.72 HA2 3.46 HG3 2.41 NH2 1.82 HE 3.25 HG2 3.48 681257 CH2 3.67 HD1 2.93 HB3 2.74 HD2 4.08 HA2 3.65 HG3 2.77 HD2 2.81 HH112.55 HG3 3.40 69 999_1 CH2 3.48 HD1 2.96 HB3 2.66 HD2 3.94 HA2 3.99 HG22.26 HD2 3.21 HD2 4.39 SD 3.11 70 999_2_A CH2 3.40 HD2 3.21 HB3 2.27 HD23.82 HA2 3.73 HG3 2.79 HH11 1.60 HH11 3.10 HG2 3.29 71 999_2_B CH2 3.40HD2 3.21 HB3 2.27 HD2 3.82 HA2 3.73 HG3 2.79 HH11 1.60 HH11 3.10 HG23.29 72 1297_1 CH2 3.63 HD2 2.85 HB3 2.48 HD2 3.78 HA2 3.45 HG2 2.30HH21 1.91 NE 3.76 HG2 3.36 73 1297_2 CH2 3.59 HD2 2.89 HB3 2.43 HD2 3.86HA2 3.52 HG3 2.40 HD2 2.03 CZ 2.94 HG2 3.16 74 1297_3 CH2 3.70 HD2 2.77HB3 2.59 HD2 3.81 HA2 3.38 HG3 2.14 HD2 2.04 CZ 2.86 HG2 3.11 75 1297_4CH2 3.59 HD2 2.91 HB3 2.43 HD2 3.87 HA2 3.52 HG3 2.26 HD2 2.07 CZ 2.94HG2 3.14 76 1297_5 CH2 3.59 HD2 2.89 HB3 2.45 HD2 3.84 HA2 3.48 HG2 2.76HD3 2.88 HH11 2.37 HG2 3.37 77 1297_6 CH2 3.70 HD2 2.77 HB3 2.58 HD23.89 HA2 3.37 HG3 2.95 HD3 2.83 HH11 2.30 HG2 3.30 78 1304 CH2 3.94 HD22.67 HB3 2.51 HD2 3.39 HA2 3.58 HG3 2.32 HH21 1.91 NE 3.62 HG2 3.59 791306_1 CH2 3.13 HD1 2.73 HB3 2.43 HG2 3.86 HA2 3.95 HG3 1.89 HB2 4.40HH11 4.30 HG2 2.63 80 1306_2 CZ2 3.55 HD2 3.00 HB3 2.50 HG2 4.35 HA23.56 HG3 2.31 HD3 3.67 HH13 3.19 SD 2.81 81 1307 CZ2 3.92 HD2 2.83 HB32.40 HD2 3.30 HA2 3.75 O 3.89 HD3 1.72 HE 3.05 O 5.28 82 1328_1 CH2 4.09HD1 2.89 HB3 2.57 HD2 3.34 HA2 3.66 HG3 1.94 HH11 2.13 CZ 3.94 HG2 3.3383 1328_2 CH2 4.11 HD1 2.88 HB3 2.57 HD2 3.42 HA2 3.60 HG3 1.97 NH1 1.93HE 3.83 HG2 3.33 84 1328_3 CH2 3.95 HD1 2.89 HB3 2.40 HD2 3.31 HA2 3.68HG3 2.39 HH11 1.88 NE 3.91 SD 3.35 85 1328_4 CH2 3.99 HD1 2.81 HB3 2.60HD2 3.35 HA2 3.67 HG3 2.56 HH11 1.79 CZ 3.88 HG2 3.37 86 1334 CZ2 3.99HD2 2.49 HB3 3.19 HG2 3.99 HA2 3.67 HA 3.22 NH1 2.39 HH21 2.89 HG3 3.3087 1335 CZ3 3.67 HD1 3.02 HB3 2.61 HD2 4.28 HA2 3.61 HG2 2.32 NH1 2.36HE 3.48 HG2 3.06 88 1338 CH2 3.95 HD2 2.71 HB3 2.70 HD2 3.97 HA2 3.41HG3 2.23 HD2 2.83 HD3 3.89 SD 3.52 89 1345_1 CZ2 3.73 HD2 3.08 HB3 1.99HG2 4.30 HA2 4.16 HG3 2.28 HB2 4.41 HH11 4.40 HG2 2.61 90 1345_2 CZ33.43 HD1 3.19 HB3 2.43 HD2 3.65 HA2 3.88 HG3 2.44 HD3 3.90 HH11 3.53 HG23.14 91 1351 CH2 3.95 HD1 2.76 HB3 3.12 HD2 4.09 HA2 3.43 HG2 2.00 NH12.02 HE 3.59 SD 3.56 92 1353 CZ2 3.88 HD2 2.80 HB2 2.14 HD2 3.40 HA23.73 HG3 3.02 HD3 1.94 HE 3.51 HG2 3.34 93 1367 CH2 3.76 HD2 2.76 HB22.49 HD2 3.60 HA2 3.45 HE3 1.19 HH11 1.94 NE 3.55 HE3 3.97 94 1371 CZ33.79 HD2 2.82 HB3 2.49 HD2 3.61 HA2 3.24 O 2.76 HH21 4.08 HH21 4.34 HE23.05 95 1372_A CZ2 3.97 HD2 2.69 HB3 2.55 HD2 3.39 HA2 3.70 HG3 2.31HH21 2.06 HE 3.50 HG2 3.43 96 1372_B CZ2 3.97 HD2 2.69 HB3 2.55 HD2 3.39HA2 3.70 HG3 2.31 HH21 2.05 HE 3.49 HG2 3.43 97 1373 CZ2 4.01 HD2 2.70HB3 2.75 HD2 3.33 HA2 3.61 HG3 2.29 HH11 1.95 HE 3.49 HG2 3.49 98 1492CZ3 3.27 HD1 3.18 HB3 2.95 HD2 3.74 HA2 3.82 HG3 2.74 HD3 2.94 HD3 3.59HG2 3.00 99 1399 CZ2 4.00 HD2 2.77 HB3 2.91 HD2 3.78 HA2 3.67 HG3 2.32NH1 1.97 HE 3.51 HG2 3.41 100 1360 CH2 3.66 HD2 2.63 HB3 3.07 HD2 4.29HA2 3.60 HG3 2.20 HH21 2.01 HE 3.56 HG2 3.42 101 1368 CZ2 4.04 HD1 3.15HB3 2.97 HD2 4.11 HA2 3.92 HG3 2.92 NH2 1.93 HE 3.35 HG3 3.55 102 1406CH2 3.90 HD2 2.59 OG 2.95 HD2 3.64 HA2 3.81 HG3 2.37 HE 3.85 HH11 2.90HG2 3.38 103 1411 CH2 3.99 HD2 2.88 HB3 2.94 HG2 3.54 HA2 3.39 HG3 2.39HH21 2.01 HE 3.43 HG2 3.39 104 1433 CZ2 3.84 HD2 2.89 HB3 2.81 HD2 4.16HA2 3.69 HG3 2.51 HD3 1.75 HE 3.17 HG2 3.37 105 1441 CZ2 4.00 HD2 2.92HB3 2.98 HD2 3.43 HA2 3.56 HG3 2.38 NH2 1.86 HE 3.44 HG2 3.34 106 1435CH2 3.79 HD2 2.76 HB3 2.95 HD2 3.69 HA2 3.54 HG3 2.37 HH21 1.91 HE 3.47HG2 3.43 107 1450_A CZ2 3.95 HD2 2.90 HB3 2.76 HD2 3.92 HA2 3.75 HG32.75 HH21 1.92 HE 3.38 HG2 3.38 108 1450_B CZ2 3.95 HD2 2.90 HB3 2.76HD2 3.92 HA2 3.75 HG3 2.75 HH21 1.92 HE 3.38 HG2 3.38 average distance3.70 3.01 2.60 3.84 3.61 2.53 2.86 3.77 3.37 standard deviation 0.230.25 0.30 0.36 0.21 0.47 0.96 0.89 0.50 minimum value 3.09 2.42 1.992.97 2.99 1.07 0.15 1.74 0.74 maximum value 4.11 3.84 3.32 4.92 4.673.89 5.37 5.84 5.28 sample size 108 108 108 108 108 108 108 108 108

1. A compound of Formula (I-1):

or a salt thereof, wherein: Cy^(1A) is unsubstituted or substituted 5-10membered heteroaryl; wherein the ring atoms of the 5-10 memberedheteroaryl forming Cy^(1A) consist of carbon atoms and 1, 2, or 3heteroatoms selected from O, N and S; wherein the substituted C₆₋₁₀ arylor substituted 5-10 membered heteroaryl forming Cy^(1A) are substitutedwith 1, 2, 3, 4 or 5 substituents each independently selected fromR^(Cy1A), halogen, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11),C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11),NR^(c11)R^(d11), NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11),NR^(c11)C(O)OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),C(═NOR^(a11))NR^(c11)R^(d11), C(═NOC(O)R^(b11))NR^(c11)R^(d11),C(═NR^(e11))NR^(c11)C(O)OR^(a11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; each R^(Cy1A) is independently selectedfrom C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl, whereinthe ring atoms of the 5-10 membered heteroaryl or 4-10-memberedheterocycloalkyl forming R^(Cy1A) consist of carbon atoms and 1, 2, 3 or4 heteroatoms selected from O, N and S, wherein each C₁₋₆ alkyl, C₂₋₆alkenyl, or C₂₋₆ alkynyl forming R^(Cy1A) is independently unsubstitutedor substituted with 1, 2 or 3 substituents independently selected fromhalogen, CN, OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11),C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R¹¹ and oxo, and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1A) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; R¹¹ is H or C₁₋₆ alkyl, C₆₋₁₀ aryl-C₁₋₆alkyl or 5-10 membered heteroaryl-C₁₋₆ alkyl, wherein the C₁₋₆ alkylforming R¹¹ is unsubstituted or substituted by 1, 2 or 3 substituentsindependently selected from halogen, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo, and wherein the C₆₋₁₀ aryl-C₁₋₆ alkyl or5-10 membered heteroaryl-C₁₋₆ alkyl forming R¹¹ is unsubstituted orsubstituted by 1, 2 or 3 substituents independently selected from C₁₋₆alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11),SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; R¹² is H or C₁₋₆ alkyl; or R¹¹ and R¹²,together with the groups to which they are attached, form a 4-6 memberedheterocycloalkyl ring; A¹¹ is CR¹³R¹⁵ or N; each R¹³ is independentlyCy^(1B), (CR^(13A)R^(13B))_(n3)Cy^(1B), (C₁₋₆ alkylene)Cy^(1B), (C₂₋₆alkenylene)Cy^(1B), (C₂₋₆ alkynylene)Cy^(1B) or OCy^(1B), wherein theC₁₋₆ alkylene, C₂₋₆ alkenylene, or C₂₋₆ alkynylene component of R¹³ isunsubstituted or substituted by 1, 2, 3, 4 or 5 substituents eachindependently selected from the group consisting of halogen, CN,OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11),OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; each R¹⁴ is independently selected from Hand C₁₋₆ alkyl; R¹⁵ is selected from H, R¹³, C₁₋₆ alkyl and OH; a pairof R¹⁴ groups attached to adjacent carbon atoms, or a pairing of R¹⁴ andR¹⁵ groups attached to adjacent carbon atoms, may, independently ofother occurrences of R¹⁴, together be replaced a bond connecting theadjacent carbon atoms to which the pair of R¹⁴ groups or pairing of R¹⁴and R¹⁵ groups is attached, such that the adjacent carbon atoms areconnected by a double bond; or a pair of R¹⁴ groups attached to the samecarbon atom, or a pairing of R¹³ and R¹⁵ groups attached to the samecarbon atom, may, independently of other occurrences of R¹⁴, andtogether with the carbon atom to which the pair of R¹⁴ groups or pairingof R¹³ and R¹⁵ groups is attached together form a spiro-fused C₃₋₁₀cycloalkyl or 4-10 membered heterocycloalkyl ring, wherein the ringatoms of the 4-10 membered heterocycloalkyl ring formed consist ofcarbon atoms and 1, 2, or 3 heteroatoms selected from O, N and S,wherein the spiro-fused C₃₋₁₀ cycloalkyl or 4-10 memberedheterocycloalkyl ring formed is optionally further substituted with 1, 2or 3 substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11),C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11),NR^(c11)R^(d11), NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11),NR^(c11)C(O)OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo; orpairs of R¹⁴ groups attached to adjacent carbon atoms, or a pairing ofR¹⁴ and R¹⁵ groups attached to adjacent carbon atoms, may, independentlyof other occurrences of R¹⁴, together with the adjacent carbon atoms towhich the pair of R¹⁴ groups or pairing of R¹⁴ and R¹⁵ groups isattached, form a fused C₃₋₁₀ cycloalkyl or 4-10 memberedheterocycloalkyl ring, wherein the ring atoms of the 4-10 memberedheterocycloalkyl ring formed consist of carbon atoms and 1, 2, or 3heteroatoms selected from O, N and S, wherein the fused C₃₋₁₀ cycloalkylor 4-10 membered heterocycloalkyl ring formed is optionally furthersubstituted with 1, 2 or 3 substituents independently selected fromhalogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, haloalkyl, CN,OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11),OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; or a grouping of four R¹⁴ groups attachedto two adjacent carbon atoms, or a grouping of two R¹⁴, one R¹³ and oneR¹⁵ groups attached to two adjacent carbon atoms, may, independently ofother occurrences of R¹⁴, together with the two adjacent carbon atoms towhich the grouping of four R¹⁴ groups or grouping of two R¹⁴, one R¹³and one R¹⁵ groups are attached, form a fused C₆₋₁₀ aryl or 5-10membered heteroaryl, C₃₋₁₀ cycloalkyl or 4-10 membered heterocycloalkylring, wherein the ring atoms of the 5-10 membered heteroaryl or 4-10membered heterocycloalkyl ring formed consist of carbon atoms and 1, 2,or 3 heteroatoms selected from O, N and S, and wherein the fused C₆₋₁₀aryl or 5-10 membered heteroaryl, C₃₋₁₀ cycloalkyl or 4-10 memberedheterocycloalkyl ring formed is optionally further substituted with 1, 2or 3 substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11),C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11),NR^(c11)R^(d11), NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11),NR^(c11)C(O)OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo; n1 is1 or 2; n2 is 0, 1 or 2; provided that the sum of n1 and n2 is 1, 2 or3; provided that if n1 is 1 or n2 is 0, then A¹¹ is CR¹³R¹⁵; n3 is 0, 1or 2; each R^(13A) is independently H or C₁₋₆ alkyl; each R^(13B) isindependently H or C₁₋₆ alkyl; or or R^(13A) and R^(13B) attached to thesame carbon atom, independently of any other R^(13A) and R^(13B) groups,together may form —(CH₂)₂₋₅—, thereby forming a 3-6 membered cycloalkylring; Cy^(1B) is unsubstituted or substituted C₆₋₁₀ aryl, unsubstitutedor substituted 5-10 membered heteroaryl, unsubstituted or substitutedC₃₋₁₀ cycloalkyl, or unsubstituted or substituted 4-10 memberedheterocycloalkyl; wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming Cy^(1B) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; and whereinthe substituted C₆₋₁₀ aryl, substituted 5-10 membered heteroaryl,substituted C₃₋₁₀ cycloalkyl or substituted 4-10 memberedheterocycloalkyl forming Cy^(1B) are substituted with 1, 2, 3, 4 or 5substituents each independently selected from R^(Cy1B), halogen, C₁₋₆haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11),C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), C(═NOR^(a11))NR^(c11)R^(d11),C(═NOC(O)R^(b11))NR^(c11)R^(d11), C(═NR^(e11))NR^(c11)C(O)OR^(a11),NR^(c11)C(═NR^(e11))NR^(c11)R^(d11), S(O)R^(b11), S(O)NR^(c11)R^(d11),S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11), S(O)₂NR^(c11)R^(d11) and oxo;wherein each R^(Cy1B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10 membered heteroaryl, C₃₋₁₀cycloalkyl and 4-10 membered heterocycloalkyl, wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingR^(Cy1B) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; wherein each C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynylforming R^(Cy1B) is independently unsubstituted or substituted with 1, 2or 3 substituents independently selected from halogen, CN, OR^(a11),SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1B) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; R¹⁶ is H, Cy^(1C), C₁₋₆ alkyl, C₂₋₆alkenyl, or C₂₋₆ alkynyl, wherein the C₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆alkynyl forming R¹⁶ is unsubstituted or substituted by 1, 2, 3, 4 or 5substituents selected from the group consisting of Cy^(1C), halogen, CN,OR^(a11), SR^(a11), C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11),OC(O)R^(b11), OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11),NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo, provided that no more than one of thesubstituents of R¹⁶ is Cy^(1C); Cy^(1C) is unsubstituted or substitutedC₆₋₁₀ aryl, unsubstituted or substituted 5-10 membered heteroaryl,unsubstituted or substituted C₃₋₁₀ cycloalkyl, or unsubstituted orsubstituted 4-10 membered heterocycloalkyl; wherein the ring atoms ofthe 5-10 membered heteroaryl or 4-10 membered heterocycloalkyl formingCy^(1C) consist of carbon atoms and 1, 2 or 3 heteroatoms selected fromO, N and S; and wherein the substituted C₆₋₁₀ aryl, substituted 5-10membered heteroaryl, substituted C₃₋₁₀ cycloalkyl or substituted 4-10membered heterocycloalkyl forming Cy^(1C) are substituted with 1, 2, 3,4 or 5 substituents each independently selected from R^(Cy1C), halogen,C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11), C(O)R^(b11),C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11), OC(O)NR^(c11)R^(d11),NR^(c11)R^(d11), NR^(c11)C(O)R^(b11), NR^(c11)C(O)NR^(c11)R^(d11),NR^(c11)C(O)OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),C(═NOR^(a11))NR^(c11)R^(d11), C(═NOC(O)R^(b11))NR^(c11)R^(d11),C(═NR^(e11))NR^(c11)C(O)OR^(a11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; wherein each R^(Cy1C) is independentlyselected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₆₋₁₀ aryl, 5-10membered heteroaryl, C₃₋₁₀ cycloalkyl and 4-10 memberedheterocycloalkyl, wherein the ring atoms of the 5-10 membered heteroarylor 4-10 membered heterocycloalkyl forming R^(Cy1C) consist of carbonatoms and 1, 2 or 3 heteroatoms selected from O, N and S; wherein eachC₁₋₆ alkyl, C₂₋₆ alkenyl, or C₂₋₆ alkynyl forming R^(Cy1C) isindependently unsubstituted or substituted with 1, 2 or 3 substituentsindependently selected from halogen, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; and wherein each C₆₋₁₀ aryl, 5-10 memberedheteroaryl, C₃₋₁₀ cycloalkyl and 4-10 membered heterocycloalkyl formingR^(Cy1C) is independently unsubstituted or substituted with 1, 2 or 3substituents independently selected from halogen, C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, C₁₋₆ haloalkyl, CN, OR^(a11), SR^(a11),C(O)R^(b11), C(O)NR^(c11)R^(d11), C(O)OR^(a11), OC(O)R^(b11),OC(O)NR^(c11)R^(d11), NR^(c11)R^(d11), NR^(c11)C(O)R^(b11),NR^(c11)C(O)NR^(c11)R^(d11), NR^(c11)C(O)OR^(a11),C(═NR^(e11))NR^(c11)R^(d11), NR^(c11)C(═NR^(e11))NR^(c11)R^(d11),S(O)R^(b11), S(O)NR^(c11)R^(d11), S(O)₂R^(b11), NR^(c11)S(O)₂R^(b11),S(O)₂NR^(c11)R^(d11) and oxo; R^(a11), R^(b11), R^(c11) and R^(d11) areeach independently selected from H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, C₆₋₁₀ aryl, C₃₋₇ cycloalkyl, 5-10 membered heteroaryl, 4-10membered heterocycloalkyl, C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 memberedheteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-10 memberedheterocycloalkyl-C₁₋₃ alkyl, wherein said C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆alkynyl, C₆₋₁₀ aryl, C₃₋₇ cycloalkyl, 5-10 membered heteroaryl, 4-10membered heterocycloalkyl, C₆₋₁₀ aryl-C₁₋₃ alkyl, 5-10 memberedheteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-10 memberedheterocycloalkyl-C₁₋₃ alkyl forming R^(a11), R^(b11), R^(c11) andR^(d11) are each optionally substituted with 1, 2, 3, 4 or 5substituents independently selected from C₁₋₆ alkyl, halo, CN, OR^(a12),SR^(a12), C(O)R^(b12), C(O)NR^(c12)R^(d12), C(O)OR^(a12), OC(O)R^(b12),OC(O)NR^(c12)R^(d12), NR^(c12)R^(d12), NR^(c12)C(O)R^(b12),NR^(c12)C(O)NR^(c12)R^(d12), NR^(c12)C(O)OR^(a12),C(═NR^(e12))NR^(c12)R^(d12), NR^(c12)C(═NR^(e12))NR^(c12)R^(d12),S(O)R^(b12), S(O)NR^(c12)R^(d12), S(O)₂R^(b12), NR^(c12)S(O)₂R^(b12),S(O)₂NR^(c12)R^(d12) and oxo; or R^(c11) and R^(d11) attached to thesame N atom, together with the N atom to which they are both attached,form a 4-, 5-, 6- or 7-membered heterocycloalkyl group or 5-memberedheteroaryl group, each optionally substituted with 1, 2 or 3substituents independently selected from C₁₋₆ alkyl, halo, CN, OR^(a12),SR^(a12), C(O)R^(b12), C(O)NR^(c12)R^(d12), C(O)OR^(a12), OC(O)R^(b12),OC(O)NR^(c12)R^(d12), NR^(c12)R^(d12), NR^(c12)C(O)R^(b12),NR^(c12)C(O)NR^(c12)R^(d12), NR^(c12)C(O)OR^(a12),C(═NR^(e12))NR^(c12)R^(d12), NR^(c12)C(═NR^(e12))NR^(c12)R^(d12),S(O)R^(b12), S(O)NR^(c12)R^(d12), S(O)₂R^(b12), NR^(c12)S(O)₂R^(b12),S(O)₂NR^(c12)R^(d12) and oxo; R^(a12), R^(b12), R^(c12) and R^(d12) areeach independently selected from H, C₁₋₆ alkyl, C₁₋₆ haloalkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 membered heteroaryl,4-7 membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6 memberedheteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7 memberedheterocycloalkyl-C₁₋₃ alkyl, wherein said C₁₋₆ alkyl, C₁₋₆ haloalkyl,C₂₋₆ alkenyl, C₂₋₆ alkynyl, phenyl, C₃₋₇ cycloalkyl, 5-6 memberedheteroaryl, 4-7 membered heterocycloalkyl, phenyl-C₁₋₃ alkyl, 5-6membered heteroaryl-C₁₋₃ alkyl, C₃₋₇ cycloalkyl-C₁₋₃ alkyl and 4-7membered heterocycloalkyl-C₁₋₃ alkyl forming R^(a12), R¹², R^(c12) andR^(d12) are each optionally substituted with 1, 2 or 3 substituentsindependently selected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxyand oxo; or R^(c12) and R^(d12) attached to the same N atom, togetherwith the N atom to which they are both attached, form a 4-, 5-, 6- or7-membered heterocycloalkyl group or 5-membered heteroaryl group, eachof which is unsubstituted or substituted with 1, 2 or 3 substituentsindependently selected from OH, CN, amino, NH(C₁₋₆ alkyl), N(C₁₋₆alkyl)₂, halo, C₁₋₆ alkyl, C₁₋₆ alkoxy, C₁₋₆ haloalkyl, C₁₋₆ haloalkoxyand oxo; and R^(e11) and R^(e12) are each, independently, H, CN or NO₂.2. The compound or salt thereof of claim 1, wherein the compound is ofFormula (I-2):


3. The compound or salt thereof of claim 1, wherein Cy^(1A) issubstituted with at least one OR^(a11), C(═NR^(e11))NR^(c11)R^(d11),C(═NOR^(a11))NR^(c11)R^(d11), C(═NOC(O)R^(b11))NR^(c11)R^(d11), orC(═NR^(e11))NR^(c11)C(O)OR^(a11).
 4. The compound or salt thereof ofclaim 1, wherein Cy^(1A) is unsubstituted or substituted pyridin-3-yl,1H-pyrrolo[2,3-b]pyridine-5-yl, or 1H-benzo[d]imidazol-6-yl.
 5. Thecompound or salt thereof of claim 1, wherein Cy^(1A) is of any one ofthe following formulae:

wherein each R^(Cy1A) attached to a carbon atom is independently C₁₋₆alkyl, halogen, or amino, and each R^(Cy1A) attached to a nitrogen atomis H or C₁₋₆ alkyl.
 6. The compound or salt thereof of claim 1, whereinR¹¹ is H or C₁₋₆ alkyl.
 7. The compound or salt thereof of claim 1,wherein R¹¹ is methyl.
 8. The compound or salt thereof of claim 1,wherein R¹² is H or C₁₋₆ alkyl.
 9. The compound or salt thereof of claim1, wherein the compound is according to any one of the followingFormulae (I-3) to (I-9):


10. The compound or salt thereof of claim 1, wherein the compound isaccording to any one of the following Formulae (I-9a) to (I-9z):


11. The compound or salt thereof of claim 10, wherein R¹³ is Cy^(1B),CH₂Cy^(1B), CH₂CH₂Cy^(1B), or OCy^(1B), and wherein Cy^(1B) issubstituted or unsubstituted C₆₋₁₀ aryl or substituted or unsubstituted5-10 membered heteroaryl.
 12. The compound or salt thereof of claim 11,wherein Cy^(1B) is substituted with 1, 2, 3, 4 or 5 substituents eachindependently selected from R^(Cy1B), halogen, and C₁₋₆ haloalkyl;wherein each R^(Cy1B) is independently selected from C₁₋₆ alkyl, C₂₋₆alkenyl, C₂₋₆ alkynyl and C₆₋₁₀ aryl or 5-10 membered heteroaryl,wherein each C₆₋₁₀ aryl or 5-10 membered heteroaryl forming R^(Cy1B) isunsubstituted or substituted with 1, 2 or 3 substituents independentlyselected from halogen, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, andhaloalkyl.
 13. The compound or salt thereof of claim 11, wherein R¹³ isa group selected from groups of the following formulae:

wherein R^(Cy1B) is H, C₁₋₆ alkyl or halogen.
 13. The compound or saltthereof of claim 1, wherein each R¹⁴ is hydrogen.
 14. The compound orsalt thereof of claim 1, wherein R¹⁵ is hydrogen.
 15. The compound orsalt thereof of claim 1, wherein R¹⁶ is hydrogen, unsubstituted orsubstituted C₁₋₆ alkyl, unsubstituted or substituted C₂₋₆ alkenyl, orunsubstituted or substituted C₂₋₆ alkynyl.
 16. A pharmaceuticalcomposition comprising a compound or pharmaceutically acceptable saltthereof of claim 1 and a pharmaceutically acceptable carrier orexcipient.
 17. A method for treating a MASP-2-associated disease ordisorder in a subject in need thereof comprising administering to thesubject an effective amount a compound or pharmaceutically acceptablesalt thereof of claim 1.